Apparatus and methods for reducing the footprint of a library preparation automation platform

Abstract

Apparatus and methods for reducing the footprint of a library preparation automation platform are disclosed. In according with an implementation, an apparatus includes a cabinet defining and enclosing a working chamber, an assay bay within the working chamber and configured to prepare a nucleic acid library for sequencing, and a consumables bay within the working chamber. A vertically oriented storage unit is positioned above a deck of the consumables bay and is configured to receive a plurality of consumable carriers. A gripper assembly is configured to move a consumable carrier of the plurality of consumable carriers between the vertically oriented storage unit and a staging area on a top surface of the deck.

Description

APPARATUS AND METHODS FOR REDUCING THE FOOTPRINT OF A LIBRARY PREPARATION AUTOMATION PLATFORMBACKGROUND

[0001] The size of current library preparation automation platforms is typically driven by the number of reagents, the number of reaction reservoirs, and the number of pipette tips required by the assay. The consumable carriers carrying these consumables are typically laid out in a horizontal plane, placed side-by-side, and are accessible to a pipettor riding on a cross-bay gantry. However, this side-by-side layout of the consumable carriers forces the XY dimensions (the footprint) of the instrument to increase when supporting more complicated workflows with more reagents, wells, and tips. This can cause the XY dimensions of the apparatus to exceed the size of a traditional lab bench, particularly the depth, and require more bench space overall.

[0002] To minimize the XY dimensions, some library preparation automation platforms use the Z dimension to stack consumable carriers, typically in motorized elevators. However, the elevators are beneath the XY working plane (deck) of the apparatus and the consumable carriers are lifted to the deck level for use. These apparatus require that the elevator extends below the deck, which significantly increases the total height of the apparatus, forces the apparatus to be floor standing, and requires a custom instrument support structure to house the elevators. This prevents the apparatus from being used on a benchtop.SUMMARY

[0003] Advantages and benefits over the prior art as described later in this disclosure can be achieved through the provision of apparatus and methods for reducing the footprint of a library preparation automation platform. Various implementations of the apparatus and methods are described below, and the apparatus and methods, including and excluding the additional implementations enumerated below, in any combination (provided these combinations are not inconsistent), may overcome these shortcomings and achieve the benefits described herein.

[0004] In accordance with a first implementation, an apparatus comprises a cabinet defining and enclosing a working chamber, an assay bay positioned in the working chamber of the cabinet and configured to prepare a nucleic acid library for sequencing, and a consumables bay positioned within the working chamber of the cabinet. A vertically oriented storage unit is positioned above a deck of the consumables bay and is configured to receive a plurality of consumable carriers. A gripper assembly is located withing the cabinet and is configured to move a consumable carrier of the plurality of consumable carriers between the vertically oriented storage unit and a staging area on a top surface of the deck of the consumables bay.

[0005] In accordance with a second implementation, an apparatus comprises a cabinet defining and enclosing a working chamber, an assay bay positioned within the working chamber of the cabinet and configured to prepare a nucleic acid library for sequencing, and a consumables bay positioned within the working chamber of the cabinet. A gripper assembly is located within the cabinet and comprises a horizontally oriented gripping apparatus. The gripper assembly is configured to engage a consumable carrier located in a vertical stack of consumable carriers positioned on a top surface of a deck of the consumable bay from a side of the consumable carrier and move the consumable carrier from the vertical stack of consumable carriers to a staging area located on the top surface of the deck.

[0006] In accordance with a third implementation, an apparatus comprises a cabinet defining and enclosing a working chamber, an assay bay positioned within the working chamber of the cabinet and configured to prepare a nucleic acid library for sequencing, and a consumables bay positioned within the working chamber of the cabinet and comprising a deck and a movable drawer. A vertically oriented storage unit is configured to receive a plurality of consumable carriers and to move between positions above the deck of the consumable bay and positions below the deck and within the movable drawer. A gripper assembly is located within the cabinet and is configured to move a consumable carrier of the plurality of consumable carriers between the vertically oriented storage unit and a staging area on a top surface of a bottom of the movable drawer.

[0007] In further accordance with the foregoing implementations, an apparatus may further include or comprise any one or more of the following:

[0008] In an implementation, the gripper assembly comprises a horizontally oriented gripping apparatus mounted on a cross-bay gantry positioned within the cabinet.

[0009] In another implementation, the apparatus comprises a pipettor and a vertically oriented gripping apparatus mounted on the cross-bay gantry.

[0010] In another implementation, the gripper assembly is mounted to the deck of the consumables bay.

[0011] In another implementation, the vertically oriented storage unit comprises a plurality of horizonal shelves, each shelf of the plurality of horizontal shelves configured to receive a consumable carrier of the plurality of consumable carriers.

[0012] In another implementation, the vertically oriented storage unit is mounted to the top surface of the deck of the consumables bay.

[0013] In another implementation, the vertically oriented storage unit comprises a plurality of movable doors, each door aligned with a shelf space above one of the plurality of horizontal shelves.

[0014] In another implementation, the vertically oriented storage unit is mounted to a movable wall of the cabinet.

[0015] In another implementation, the movable wall of the cabinet comprises a plurality of movable doors, each door aligned with a shelf space above one of the plurality of horizontal shelves.

[0016] In another implementation, the vertically oriented storage unit comprises a plurality of drawers, each of the drawers configured to receive a consumable carrier of the plurality of consumable carriers.

[0017] In another implementation, the vertically oriented storage unit is mounted to a top surface of the deck of the consumables bay.

[0018] In another implementation, the vertically oriented storage unit is mounted to a movable wall of the cabinet.

[0019] In another implementation, the movable wall of the cabinet comprises a plurality of movable doors, each door aligned with a drawer of the plurality of drawers.

[0020] In another implementation, the gripper assembly is configured to move the consumable carrier from the staging area to a discard area.

[0021] In another implementation, a lift mechanism is operatively connected to the vertically oriented storage unit and is configured to move the vertically oriented storage unit between the positions above the deck and positions below the deck and within the movable drawer.

[0022] In accordance with a fourth implementation, a method comprises: receiving a plurality of consumable carriers in a vertically oriented storage unit positioned above a deck of a consumables bay, the consumables bay being positioned within a working chamber defined and enclosed by a cabinet; preparing a nucleic acid library for sequencing in an assay bay positioned with the working chamber of the cabinet; removing a consumable carrier of the plurality of consumable carriers from the storage unit using a gripper assembly located within the cabinet; and placing the consumable carrier removed from the storage unit onto a staging area on the deck of the consumables bay using the gripper assembly.

[0023] In accordance with a fifth implementation, a method comprises: receiving a vertical stack of consumable carriers on a top surface of a deck of a consumables bay, the consumables bay being positioned within a working chamber defined and enclosed by a cabinet; preparing a nucleic acid library for sequencing in an assay bay positioned with the working chamber of the cabinet; engaging a consumable carrier of the stack of consumable carriers from a side of the consumable carrier and removing the consumable carrier from the vertical stack of consumable carriers using a gripper assembly located within the cabinet, the gripper assembly comprising a horizontally oriented gripping apparatus; and placing the consumable carrier removed from the vertical stack of consumable carriers onto a staging area on the deck of the consumables bay using the gripper assembly.

[0024] In accordance with a sixth implementation, a method comprises receiving a plurality of consumable carriers in a vertically oriented storage unit configured to movebetween positions above a deck of a consumables bay and positions below the deck and within a movable drawer of the consumables bay, the consumables bay being positioned within a working chamber defined and enclosed by a cabinet; preparing a nucleic acid library for sequencing in an assay bay positioned with the working chamber of the cabinet; removing a consumable carrier of the plurality of consumable carriers from the storage unit using a gripper assembly located within the cabinet; and placing the consumable carrier removed from the storage unit onto a staging area on a top surface of a bottom of the movable drawer using the gripper assembly.

[0025] In further accordance with the foregoing implementations, a method may further include or comprise any one or more of the following:

[0026] In an implementation, the method comprises removing the consumable carrier from the staging area and placing the consumable carrier into the storage unit.

[0027] In another implementation, the method comprises removing the consumable carrier from the staging area and placing the consumable carrier in a discard area using the gripper assembly.

[0028] In another implementation, the gripper assembly comprises a horizontally oriented gripping apparatus mounted on a cross-bay gantry positioned within the cabinet.

[0029] In another implementation, a pipettor and a vertically oriented gripping apparatus are mounted on the cross-bay gantry.

[0030] In another implementation, the gripper assembly is mounted to the deck of the consumables bay.

[0031] In another implementation, the method comprises loading the plurality of consumable carriers onto a plurality of horizonal shelves of the vertically oriented storage unit.

[0032] In another implementation, the method comprises loading the plurality of consumable carriers onto the plurality of horizonal shelves via a plurality of movable doors in the vertically oriented storage unit .

[0033] In another implementation, the method comprises loading the plurality of consumable carriers onto the plurality of horizontal shelves via a plurality of movable doors in a movable wall of the cabinet.

[0034] In another implementation, the method comprises loading the plurality of consumable carriers into a plurality of drawers of the vertically oriented storage unit.

[0035] In another implementation, the method comprises loading the plurality of consumable carriers into the plurality of drawers via a plurality of movable doors in a movable wall of the cabinet.BRIEF DESCRIPTION OF THE DRAWINGS

[0036] FIG. 1 illustrates a schematic diagram of an implementation of a system that can be used with the apparatus and methods for reducing the footprint of a library preparation automation system in accordance with the teachings of this disclosure;

[0037] FIG. 2 is a perspective view of a first implementation of an apparatus that can be used to implement the system of Fig. 1 ;

[0038] FIG. 3 illustrates a side view of a first implementation of a consumables bay that can be used in the apparatus of Fig. 2;

[0039] FIG. 4 illustrates a side view of a second implementation of a consumables bay that can be used in the apparatus of Fig. 2;

[0040] FIG. 5 illustrates a side view of a third implementation of a consumables bay that can be used in the apparatus of Fig. 2;

[0041] FIG. 6 illustrates a side view of a fourth implementation of a consumables bay that can be used in the apparatus of Fig. 2;

[0042] FIG. 7 illustrates a side view of a fifth implementation of a consumables bay that can be used in the apparatus of Fig. 2;

[0043] FIG. 8 illustrates a side view of a sixth implementation of a consumables bay that can be used in the apparatus of Fig. 2;

[0044] FIG. 9 is a perspective view of a second implementation of an apparatus that can be used to implement the system of Fig. 1 ;

[0045] FIG. 10 illustrates a side view of a first implementation of a consumables bay that can be used in the apparatus of Fig. 9;

[0046] FIG. 11 illustrates a side view of a second implementation of a consumables bay that can be used in the apparatus of Fig. 9;

[0047] FIG. 12 is a flow diagram of a first implementation of a method for reducing the footprint of a library preparation automation platform using the apparatus of Figs. 2-6;

[0048] FIG. 13 is a flow diagram of a second implementation of a method for reducing the footprint of a library preparation automation platform using the apparatus of Figs. 2 and 7-8; and

[0049] FIG. 14 is a flow diagram of a third implementation of a method for reducing the footprint of a library preparation automation platform using the apparatus of Figs. 9-11 .DETAILED DESCRIPTION

[0050] Although the following text discloses a detailed description of implementations of apparatus, it should be understood that the legal scope of the property right is defined by the words of the claims set forth at the end of this patent. Accordingly, the following detailed description is to be construed as examples only and does not describe every possible implementation, as describing every possible implementation would be impractical, if not impossible. Numerous alternative implementations can be implemented, using either current technology or technology developed after the filing date of this patent. It is envisioned that such alternative implementations would still fall within the scope of the claims.

[0051] In the implementations shown and discussed herein, the library prep automation platform uses the vertical space above the base of the cabinet, rather than space below the base or horizontal space on the base of the cabinet, for stacks of consumable carriers. This allows reduces the XY footprint of the apparatus and allows the apparatus to be used on a benchtop.

[0052] A stack of consumable carriers or a vertically oriented storage unit having shelves, and possible drawers, for consumable carriers is placed on a deck of one of the bays and a gripper assembly, either standalone or mounted to the cross-bay gantry, moves theconsumables to a staging location, which positions the consumable carrier at the correct deck height where it is accessible for the pipettor on the cross-bay gantry. This arrangement maintains the same overall height of the apparatus and allows for a bench top apparatus. Using shelves allows each consumable carrier to be accessed individually, which can be beneficial when the consumable carriers contain different types of consumables (e.g., plates, low volume pipette tips, large volume pipette tips, etc.). Using shelves also removes the need to discard empty consumable carriers in order to access another consumable carrier underneath.

[0053] One advantage of using a gripper assembly mounted to the cross-bay gantry is that it can share the swept volume of the cross-bay gantry for the pipettor, which directly contributes to reducing instrument size.

[0054] If the gripper assembly is a standalone gripper assembly, the gripper assembly could move out of the way in the Y direction into an empty shelf or slot in the vertically oriented storage unit to hide the gripper to allow the pipettor to reach pipettes on the row closest to the user.

[0055] Referring to Fig. 1 , a system 500 is illustrated that may be used to automatically, easily, and efficiently prepare DNA libraries for sequencing applications. System 500 may prepare the libraries when performing workflows such as whole genome sequencing workflows, DNA & RNA enrichment workflows, methylation workflows, split-pool amplicon workflows, amplicon workflows, etc. The workflows may include one or more steps, such as amplification processes, cleanup processes, quantification processes, library normalization processes, pooling processes, denaturing processes, and / or diluting processes in some implementations.

[0056] System 500 may include a controller 502, which may be electrically and / or communicatively coupled to one or more components of the system 500 to perform various functions as described herein. Controller 502 may include a user interface 504, a communication interface 506, one or more processors 508, and a memory 510 storinginstructions executable by the one or more processors 508 to perform the various functionalities described herein.

[0057] User interface 504 may receive input from a user, and provide information to the user associated with the operation of system 500 (e.g., information about the workflows being scheduled and / or taking place). User interface 504 may include a touch screen, a display, a keyboard, a speaker(s), a mouse, a track ball, a voice recognition system, etc. The touch screen and / or the display may display a graphical user interface (GUI).

[0058] Communication interface 506 can enable communication between system 500 and one or more components, such as a remote system(s) e.g., computers) using one or more network(s). The network(s) may include an intranet, a local-area network (LAN), a wide-area network (WAN), the intranet, etc. Some of the communications may be associated with workflows of system 500, such as scheduling one or more workflows.

[0059] System 500 may include one or more processors 508 and / or processor-based system(s) or a microprocessor-based system(s). In some implementations, processor(s) 508 and / or system 500 may include a reduced-instruction set computer(s) (RISC), an application specific integrated circuit(s) (ASICs), a field programmable gate array(s) (FPGAs), a field programmable logic device(s) (FPLD(s)), a logic circuit(s), and / or another logic-based device executing various functions including the ones described herein. User interface 504, communication interface 506, and memory 510 may be electrically and / or communicatively coupled to processor(s) 508.

[0060] Memory 510 may include one or more of a hard disk drive, a flash memory, a readonly memory (ROM), erasable programmable read-only memory (EPROM), electrically erasable programmable read-only memory (EEPROM), a random-access memory (RAM), non-volatile RAM (NVRAM) memory, a compact disk (CD), a digital versatile disk (DVD), a cache, and / or any other storage device or storage disk in which information is stored for any duration e.g., permanently, temporarily, for extended periods of time, for buffering, for caching, etc.).

[0061] Memory 510 may include a scheduler 512, which may be stored as instructions on memory 510 and executable by processor 508. Scheduler 512 may include a common resource schedule which is used to schedule and / or execute (e.g., by controller 502) one or more workflows. Scheduler 512 may receive a workflow request associated with one or more working areas 516, 518 and schedule the workflow to a common resource schedule. The common resource schedule may be used schedule and / or execute e.g., via controller 502) one or more workflows which utilize the second working area 518. Scheduler 512 or another suitable component e.g., processor 508) may be configured to determine one or more conflicts in time and / or space with respect to second working area 518 for at least two workflows associated with respective working areas 516, as further described herein. While scheduler 512 is described as scheduling new workflows to a common resource schedule, in at least some aspects scheduler 512 may also evaluate an existing workflow schedule and / or common resource schedule, to make optimizations and the like, as one having skill in the art will appreciate.

[0062] System 500 may include one or more consumables areas 514, one or more first working areas 516, a second working area 518, and a loading area 520.

[0063] The consumable area 514 may be used to load and store reagents and consumables needed for a library preparation process, including, disposable tips {e.g., disposable tips 338), wet or dry assay specific reagents, wet or dry bulk reagents, and reaction plates and wells {e.g., sample plates 304), etc. Consumables area 514 may include a consumables receptacle 522 which may include a tip tray 524 having a first tip 526 and a second tip 528, a first plate 530 having a well 532 containing a sample 534, and a second plate 536 having a well 538. In at least some embodiments, one or more of the working areas 516, 518 may include a consumables area.

[0064] The consumables receptacle 522 may be a drawer {e.g., movable drawer 270) that can be pulled out from system 500 and loaded with consumables 524, 526, 528, 530, 536. Consumables receptacle 522 may also include a lid 540, an index tray 542 having a well 544 containing indexes 546, a bead tray 548 having a well 550 containing beads 552, a liquidreservoir 554, and a dry reagent reservoir 556. One or more reagents 546 and / or 552 may be lyophilized and included with the dry reagent reservoir 556. In at least some aspects, one or more of the plates e.g., plates 530, 536), index tray 542, and / or bead tray 548 may be stacked. Tip tray 524 may have a plurality of the first tips 526, a plurality of the second tips 528, and / or any suitable number of tips 526, 528. Tips 526, 528 may be different sizes and may be reusable for at least multiple portions of a workflow.

[0065] First working area 516 may include a contact dispenser 558, a stage 560, a magnet 562, and a thermocycler 564. Second working area 518 may include an analyzer area 566 e.g., to analyze samples), a contact dispenser 568 and a stage 570, one or more of which can operate in and / or in conjunction with first working area 516 and second working area 518.

[0066] Contact dispenser 558 may be movable to aspirate / dispense liquid to consumables area 514 and / or to first working area 516. Contact dispenser 568 may be movable to aspirate / dispense liquid to consumables area 514, to first working area 516, and / or to second working area 518. Contact dispenser 568 may carry one or more tips, e.g., to hold a volume of fluid.

[0067] System 500 may include a mover 572, which in some aspects may be considered as part of second working area 518. Mover 572 may include a robotic arm and / or include grippers. Stage 570 may carry mover 572 and contact dispenser 568 in some implementations. Mover 572 may include a gantry having grippers that can pick-and-place objects such as plates 530, 536 and / or trays 542, 548 between different areas 516, 518, 520 of system 500, e.g., mover 572 may move first plate 536 from consumables area 514 to first plate receptacle 574. Mover 572 may be implemented in different ways, however.

[0068] Stage 560 may be an X-Z stage, such that stage 560 is movable in the X and Z directions (but not in the Y direction). Stage 560 and contact dispenser 558 may be movable to aspirate and / or dispense fluid between and above consumables area 514 and first working area 516 as a result. Contact dispenser 558 may, for example, move linearly in the X direction, which thereby reduces the risk of cross-contamination (between different samples) and allowssome or all of the tips employed in system 500 to be reusable for at least part of the processes performed by system 500. Stage 560 may be implemented differently, however.

[0069] Stage 560 may align contact dispenser 558 with tip tray 524 and contact dispenser 558 couples with first tip 526 from tip tray 524. While contact dispenser 558 is mentioned coupling with one first tip 526, contact dispenser 558 may couple with a number of first tips 526 that corresponds to the number of wells 532 in first plate 530 and / or the number of wells 532 in first plate 530 containing sample(s) 534. Wells 532 may contain different samples 534, such as a biological sample derived from a human, animal, plant, bacteria, virus, or fungi. First tip 526 may be a smaller pipette tip that is used to move smaller fluid volumes and second tip 528 may be a larger pipette tip that is used to move larger fluid volumes. Each of first tip 526 and / or second tip 528 may be exposed to a single sample during a workflow reducing the likelihood of cross-contamination and reducing the need to obtain a new tip after each operation. In some library preparation workflows, each of first tip 526 and / or second tip 528 may be used through an entire workflow. Contact dispenser 558 may couple with and / or use different ones of tips 526, 528 depending on the workflow and / or the processes within a workflow that system 500 is implementing.

[0070] Stage 570 may be an X-Y-Z stage, such that mover 572 is movable in the X, Y, and Z directions. Stage 570 and contact dispenser 568 may be movable to aspirate and / or dispense fluid between and above consumables area 514, first working area 516, and / or second working area 518 as a result. Contact dispenser 568 may, for example, move linearly in the X direction, which thereby reduces the risk of cross-contamination (between different samples) and allows some or all of the tips employed in system 500 to be reusable for at least part of the processes performed by system 500. However, stage 560 may be implemented differently.

[0071] Second working area 518 may include a light bar 576 that may be used to degrade oligonucleotides, such as a high power ultraviolet light (UV) light bar that is regularly used throughout a workflow to repeatedly degrade oligonucleotides to deter cross contamination in some implementations.

[0072] First working area 516 may include a first plate receptacle 574 and a second plate receptacle 578, second working area 518 may include a third plate receptacle 580, a fourth plate receptacle 582, and a fifth plate receptacle 584, and analyzer area 566 may include a substrate 586 and an imaging system 588, in at least some implementations. For example, analyzer area 566 may use substrate 586 that is implemented by a well plate in which a portion of the sample and a dye are dispensed, and imaging system 588 may image the portion of the sample in the well plate to determine a concentration of the sample.

[0073] Second working area 518 may include a reagent receptacle 590 having an access opening 592. A reagent reservoir 594 is shown received within reagent receptacle 590. First working area 516 may additionally or alternatively include a reagent receptacle having an access opening. Reagent receptacle 590 may be refrigerated and may be a drawer that can be pulled out from system 500 and loaded with reagent reservoir 594. Reagent reservoir 594 may be accessed through access opening 592 by contact dispenser 568 to aspirate reagent from reagent reservoir 594.

[0074] Loading area 520 may be associated with loading and / or transferring a prepared sample to a system such as a sequencing system. For example, first working area 516 may be associated with amplification processes and cleanup processes and second working area 518 may be associated with quantification processes, library normalization processes, pooling processes, denaturing processes, and / or diluting processes. Loading area 520 may include a sipper manifold assembly 596 in the implementation shown. Sipper manifold assembly 596 may include sippers 598 to couple sipper manifold assembly 596 to a corresponding number of flow cells. Sipper manifold assembly 596 may include a valve 600 to control the flow of fluid through a fluidic line 602. Sipper manifold assembly 596 may include a pump 604 to selectively flow the prepared sample from a well 538, 606 through sipper 598, through fluidic line 602, and out of system 500, e.g., to another system used to perform an analysis on one or more samples of interest.

[0075] Valve 600 may be implemented by a rotary valve, a pinch valve, a flat valve, a solenoid valve, a check valve, a piezo valve, etc. Other fluid control devices may provesuitable. Pump 604 may be implemented by a syringe pump, a peristaltic pump, and / or a diaphragm pump. Other types of fluid transfer devices may be used. Controller 502 is electrically and / or communicatively coupled to components of system 500 to perform various functions as disclosed herein. Sipper manifold assembly 596 may alternatively be omitted.

[0076] An actuator 608 can move magnet 562 between an upward position where magnet 562 affects any plate positioned on first plate receptacle 574 and a downward position where magnet 562 does not affect any plate positioned on first plate receptacle 574. Magnet 562 being moved relative to first plate receptacle 574 and any plate 530, 536, 610 positioned on first plate receptacle 574 allows less area on first working area 516 to be consumed. Magnet 562 can moreover be moved with relatively higher confidence as compared to an alternative approach to moving one of the plates 530, 536, 610 filled with samples to a separate magnet station. Magnet 562 may be implemented by a Halbach array configuration to strengthen and focus the corresponding magnetic fields.

[0077] In one example workflow, stage 560 aligns contact dispenser 558 with index tray 542 and contact dispenser 558 aspirates indexes 546 from index tray 542 using first tip 526. Stage 560 can then align contact dispenser 558 with first plate 530 and contact dispenser 558 dispenses indexes 546 into well 532 of first plate 530. Mover 572 moves lid 540 from consumables area 514 and places lid 540 on first plate 530 to cover well 532 of first plate 530 with lid 540. First working area 516 also includes a lid 612 and an actuator 614. Lid 612 may be referred to as a cover and / or a door. Actuator 614 may move lid 612 in operation relative to plate receptacle 578, for example, to cover plate receptacle 578 during amplification processes. Lid 612 may thus be positioned to enclose first plate 530 during the amplification processes. Lid 540 and / or lid 612 may enclose first plate 530 during the amplification processes.

[0078] Thermocycler 564 is aligned with first plate receptacle 578 and thermocycler 564 amplifies sample 534 within well 532 of first plate 530. Thermocycler 564 and / or magnet 562 can act on a plate 530, 536 received at first plate receptacle 578 in the implementation shown. Thermocycler 564 may alternatively be spaced from magnet 562.

[0079] Actuator 614 can move lid 612 off of first plate 530 and / or mover 572 can move lid 540 from first plate 530 to consumables area 514 after the amplification processes are complete. Consumables area 514 includes a waste 616 that can receive used consumables such as, for example, lid 540. Lid 540 may alternatively be reused. Waste 616 may be a waste tray having an absorbent material to absorb liquid waste.

[0080] System 500 may perform cleanup processes, according to one or more workflows, after the amplification processes are performed. Stage 560 aligns contact dispenser 558 with bead tray 548 and contact dispenser 558 aspirates beads 552 from bead tray 548. Contact dispenser 558 may aspirate beads 552 using the same first tip 526 used to aspirate indexes 546. Contact dispenser 558 may alternatively use another one of first tips 526 or one of second tips 528 to aspirate beads 552.

[0081] Stage 560 aligns contact dispenser 558 with first plate 530 and contact dispenser 558 dispenses beads 552 into well 532 of first plate 530 as part of the cleanup process. Stage 560 aligns contact dispenser 558 with liquid reservoir 554 and contact dispenser 558 aspirates first reagent 618 from liquid reservoir 554. Stage 560 then aligns contact dispenser 558 with first plate 530 and contact dispenser 558 dispenses first reagent 618 into well 532 of first plate 530. Contact dispenser 558 may alternatively aspirate hydrating liquid 620 from liquid reservoir 554 and then dispense hydrating liquid 620 into dried reagent 622 contained within dry reagent reservoir 556 to rehydrate dried reagent 622 and form first reagent 618. Contact dispenser 558 may pipette mix dried reagent 622 and hydrating liquid 620. First reagent 618 may be a bead buffer and sample 534 may bind to beads 552 in the presence of the bead buffer. Contact dispenser 558 may be able to jet dispense with adequate liquid velocity to enable jet mixing in some implementations. System 500 may also include a shaker to enable mixing.

[0082] Stage 560 aligns contact dispenser 558 with tip tray 524 and contact dispenser 558 places first tip 526 in tip tray 524 and contact dispenser 558 then couples with second tip 528 from tip tray 524. While contact dispenser 558 is mentioned coupling with one second tip 528, contact dispenser 558 may couple with a number of second tips 528 that corresponds to thenumber of wells 532 in first plate 530 and / or the number of wells 532 in first plate 530 containing the sample 534.

[0083] Actuator 608 moves magnet 562 toward plate receptacle 578 and magnet 562 draws beads 552 toward magnet 562. Beads 552 and sample 534 bound to beads 552 may be positioned toward the bottom of well 532 of first plate 530 or on a side(s) of well 532. Tips 526 and / or 528 may easily access well 532 if beads 552 are on the side of well 532. Magnet 562 may cause beads 552 to be in any position within well 532.

[0084] Stage 560 aligns contact dispenser 558 with first plate 530 and contact dispenser 558 aspirates first reagent 618 from well 532 of first plate 530. Contact dispenser 558 may dispense first reagent 618 aspirated from well 532 of first plate 530 into waste 616.

[0085] Stage 560 aligns contact dispenser 558 with liquid reservoir 554 and contact dispenser 558 aspirates second reagent 624 from liquid reservoir 554 and stage 560 then aligns contact dispenser 558 with first plate 530 and contact dispenser 558 dispenses second reagent 624 into well 532 of first plate 530. Contact dispenser 558 may alternatively aspirate hydrating liquid 620 from liquid reservoir 554 and then dispense hydrating liquid 620 into a dried reagent 626 contained within dry reagent reservoir 556 to rehydrate dried reagent 626 and form second reagent 624. Second reagent 624 may be an elution buffer that releases sample 534 from being bound to beads 552 and, specifically, releases DNA associated with sample 534 from being bound to beads 552.

[0086] Mover 572 moves second plate 536 from consumables area 514 to second plate receptacle 578. System 500 can use second plate 536 for a transfer operation. Second plate 536 may alternatively remain in consumables area 514 during the transfer operation. Actuator 608 moves magnet 562 toward second plate receptacle 578 to draw beads 552 toward magnet 562 and, thus, provide a substantially bead-free eluate solution comprising second reagent 624 and sample 534 within well 532.

[0087] Stage 560 can align contact dispenser 558 with first plate 530 and contact dispenser 558 aspirates second reagent 624 and sample 534 from well 532 of first plate 530 using second tip 528. Stage 560 aligns contact dispenser 558 with second plate 536 andcontact dispenser 558 dispenses second reagent 624 and sample 534 into well 538 of second plate 536. Second plate 536 may alternatively be positioned in consumables area 514 when contact dispenser 558 dispenses second reagent 624 and sample 534 into well 538 of second plate 536. Second plate receptacle 578 may be omitted from second working area 518 in such implementations.

[0088] System 500 may perform the quantification processes, according to one or more workflows, after the cleanup processes are performed. Mover 572 moves second plate 536 from first working area 516 to plate receptacle 580 of second working area 518 to initiate the quantification processes in some implementations. Mover 572 may alternatively move second plate 536 from consumables area 514 to plate receptacle 580 of second working area 518 to initiate the quantification processes in implementations when second plate 536 remains in consumables area 514 during the transfer operations. Stage 570 aligns contact dispenser 568 with tip tray 524 of second working area 518 in some implementations and contact dispenser 558 couples with a tip 628 from tip tray 524.

[0089] Substrate 586 may be a plate having a well. Substrate 586 may be a consumable that is disposed of after use. Imaging system 588 may be spaced from substrate 586 and coupled to a portion of system 500 such as a frame of system 500. Imaging system 588 may alternatively be carried by a stage.

[0090] Stage 570 aligns contact dispenser 568 with second plate 536 to perform the quantification processes and contact dispenser 568 aspirates a portion of second reagent 624 and sample 534 from well 538 of second plate 536. The portion of second reagent 624 and sample 534 may be about 2pL.

[0091] Stage 570 aligns contact dispenser 568 with substrate 586 and contact dispenser 568 dispenses the portion of second reagent 624 and sample 534 into a well of substrate 586 as an example. A dye may also be dispensed into the well of substrate 586 by contact dispenser 568. Imaging system 588 obtains image data of the portion of second reagent 624 and sample 534 within the well of substrate 586. Imaging system 588 and / or system 500 usesthe image data to determine a concentration of sample 534. Mover 572 may move substrate586 to waste 616 of consumables area 514 of second working area 518.

[0092] Substrate 586 may alternatively be implemented by a pair of plates 634, 636 between which a gap 638 is defined. Substrate 586 in such an implementation includes an inlet 640 and an outlet 642 in fluid communication with gap 638 and a seal 644 positioned between the pair of plates 634, 636. Plates 634, 636 and seal 644 define a channel 646 between inlet 640 and outlet 642. A waste reservoir 648 may be fluidly coupled to outlet 642 of substrate 586 by a fluidic line 650.

[0093] In the alternative implementation of substrate 586, stage 570 aligns contact dispenser 568 with inlet 640 of substrate 586 and contact dispenser 568 dispenses the portion of second reagent 624 and sample 534 into inlet 640 of substrate 586. The portion of second reagent 624 and sample 534 may flow and / or be positioned between inlet 640 and outlet 642 in this implementation and imaging system 588 obtains image data of the portion of second reagent 624 and sample 534. Imaging system 588 and / or system 500 uses the image data to determine a concentration of sample 534. Negative pressure, oil, and / or another substance may be used to urge the portion of second reagent 624 and sample 534 between inlet 640 and outlet 642. First plate 634 may alternatively be hingably coupled or removably coupled to second plate 636 to allow contact dispenser 568 to dispense the portion of second reagent 624 and sample 534 onto second plate 636 prior to first plate 634 being positioned overtop of second plate 636. However, system 500 may perform quantification processes in different ways.

[0094] System 500 may perform the normalization processes, according to one or more workflows, after the quantification processes are performed. Stage 570 aligns contact dispenser 568 to initiate the normalization processes in some implementations. Contact dispenser 568 aspirates a diluent 654 from a liquid reservoir 652 of second working area 518. Stage 570 then aligns contact dispenser 568 with second plate 536 and contact dispenser 568 dispenses diluent 654 into well 538 of second plate 536 to dilute sample 534 based on the concentration of the sample determined. Sample 534 within well 538 of second plate 536 willhave a concentration within a threshold value after diluent 654 is added to well 538 as a result.Diluent 654 may be a buffer.

[0095] System 500 may perform the pooling processes, according to one or more workflows, after the quantification processes are performed. Stage 570 aligns contact dispenser 568 with tip tray 524 of second working area 518 and contact dispenser 568 places tip 628 in tip tray 524 and contact dispenser 568 then couples with another tip 630 from tip tray 524 to initiate the pooling processes in some implementations. Mover 572 moves a plate 610 from second working area 518 to plate receptacle 582 of second working area 518. Stage 570 aligns contact dispenser 568 with second plate 536 and contact dispenser 568 aspirates sample 534 from well 538 of second plate 536. Stage 570 then aligns contact dispenser 568 with third plate 610 and contact dispenser 568 dispenses sample 534 into well 606 of the third plate 610. Additional samples from other wells of second plate 536 may be deposited into well 606 of third plate 610 in a similar manner to combine a plurality of normalized samples together. A single tip can be used for the pooling processes. Contact dispenser 568 may pipette from final archive library well directly to pool and, thus, unique tips per sample may be used.

[0096] System 500 may perform the denaturing processes, according to one or more workflows, after the pooling processes are performed (though in some implementations, denaturing need not be performed). Stage 570 aligns contact dispenser 568 with tip tray 524 of second working area 518 and contact dispenser 568 places tip 630 in tip tray 524 and contact dispenser 568 then couples with another tip 632 from tip tray 524 to initiate the denaturing processes in some implementations. Contact dispenser 568 may use the same tip 630 used during the pooling processes in some implementations. Stage 570 aligns contact dispenser 568 with liquid reservoir 652 and contact dispenser 568 aspirates reagent 656 from liquid reservoir 652. Stage 570 then aligns contact dispenser 568 with third plate 610 and contact dispenser 568 dispenses reagent 656 into well 606 of third plate 610 to denature the pooled and normalized samples. Reagent 656 may be Sodium hydroxide (NaOH). Otherdenaturing processes may prove suitable. For example, Formamide or an equivalent may be used during the denaturing processes.

[0097] System 500 may dilute the pooled and denatured samples, according to one or more workflows, after the pooling and the denaturing processes are performed. Contact dispenser 568 aspirates diluent 654 from liquid reservoir 652 of second working area 518. Stage 570 then aligns contact dispenser 568 with third plate 610 and contact dispenser 568 dispenses diluent 654 into well 538 of third plate 610 to dilute sample 534 based on the concentration of the sample based on specifications of the sequencing system into which the sample is to be loaded. The pooled samples 534 within well 606 of third plate 610 will have a concentration within a threshold value after diluent 654 is added to well 606 as a result. Diluent 654 may be a buffer.

[0098] System 500 may perform the loading processes, according to one or more workflows, after the denaturing processes and / or after the diluting processes are performed. Mover 572 moves third plate 610 from second working area 518 to a plate receptacle 658 of loading area 520. Loading area 520 is shown including a stage 660 that can be used to move plate receptacle 658 relative to sipper manifold assembly 596. Sipper manifold assembly 596 flows the denatured samples from well 538, 606 through the corresponding sipper(s) 598, through the fluidic line(s) 602, and out of system 500 to another system for sequencing.

[0099] System 500 also includes a drive assembly 662. Drive assembly 662 includes a pump drive assembly 664 and a valve drive assembly 666. Pump drive assembly 664 may be adapted to interface with pump 604 to pump fluid from reagent reservoir 594 to a noncontact dispenser. Valve drive assembly 666 may be adapted to interface with valve 600 to control the position of the valve 600.

[0100] In some aspects, more or fewer instances of the various components of the system 500 shown in FIG. 1 may be included in system 500 (e.g., four working areas , three consumable areas, etc.).

[0101] Referring to Fig. 2, a first implementation of an apparatus 100A is illustrated that can be used to implement system 500. Apparatus 100A can be used to automatically, easily,and efficiently prepare DNA libraries for sequencing applications. Apparatus 100A may perform DNA library preparation workflows that include amplification processes, cleanup processes, quantification processes, library normalization processes, pooling processes, denaturing processes, diluting processes, etc., and can perform a number of workflows at the same time and / or at different times. In the implementation shown, apparatus 100A generally includes a cabinet 102 that defines and encloses a working chamber 1 10 and a plurality of assay bays 200, at least one consumables bay 300, and at least one transfer bay 400 positioned within working chamber 110.

[0102] Cabinet 102 generally includes a base 104, a frame 106 mounted to base 104, and walls 108 (e.g., a front wall, rear wall, side walls, and top wall) supported by frame 106. Walls 108 of cabinet 102 are transparent or opaque e.g., glass, plexiglass, sheet metal, etc.) and together with base 104 and frame 106 define and enclose working chamber 1 10. Walls 108 can include at least one movable wall 108A e.g., a front wall located on a front 1 18 of apparatus 100A) that can be moved to provide a user access to working chamber 1 10 of cabinet 102. In one implementation, movable wall 108A can be hingedly connected on one side to frame 106 to allow movable wall 108A to be opened like a door.

[0103] A cross-bay gantry 122 can be secured to base 104 and positioned within working chamber 1 10. Cross-bay gantry 122 is movable in the X, Y, and Z directions. Cross-bay gantry 122 can include a pipettor 124 and a vertically oriented gripping apparatusl 26 mounted to cross-bay gantry 122. Pipettor 124 can be configured to aspirate / dispense liquid between locations within assay bays 200, between locations within consumables bay 300, between locations within transfer bay 400, and / or to locations between assay bays 200, consumables bay 300, and transfer bay. Vertically oriented gripping apparatus 126 is configured to approach / engage objects from the top / above the objects and pick-and-place the objects, such as plates and / or the trays, between different locations.

[0104] Each assay bay 200 can be configured to prepare nucleic acid libraries for sequencing and can be configured to asynchronous operation. In the implementation shown, each assay bay 200 includes a deck 202 and a thermocycler 204 positioned on deck 202.Thermocycler 204 can include a stage 206 that is movable in the X and Z directions (but not in the Y direction) and that is movable to aspirate and / or dispense fluid within thermocycler 204. Each assay bay 200 also includes a pipette assembly 208 that is movable in the Y and Z directions and is configured to aspirate / dispense liquid between locations within the particular assay bay 200 and a drawer 210 that is movably mounted to deck 202 and is movable between a closed position and an open position. In the open position, drawer 210 can be loaded with and store various consumables, such as large liquid reagents 212, small liquid reagents 214, Lyo reagents 216, sample plates 218 (e.g., sample plates, reaction plates and wells, etc.), disposable tips 220, etc., that may be needed for a library prep process on a bottom 222 of drawer 210.

[0105] Transfer bay 400 can be used for loading and / or transferring a prepared sample to a system such as a sequencing system and / or next generation sequencing system and can be positioned adjacent a second side of the plurality of assay bays 200, opposite consumables bay 300 on a first side. In the implementation shown, transfer bay 400 can include a deck 402 and quant station 404 positioned on deck 402. Deck 402 of transfer bay 400 can also be loaded with and store various consumables, such as D&D Pool Strips 406, disposable tips 408, etc., that may be needed for a library prep process on deck 402.

[0106] Referring to Fig. 3, a first implementation of consumables bay 300A is illustrated in apparatus 100A, which can be used to reduce the footprint of apparatus 100A. In alternative embodiments, the structure described herein for use in consumables bay 300A can also be used in assay bay 200 and / or transfer bay 400.

[0107] Consumables bay 300A includes a deck 302 that is positioned on base 104 of cabinet 102 and can be positioned adjacent a first side of the plurality of assay bays 200. Consumables bay 300A can be bulk loaded with and store consumables, preferably noncontamination risk consumables, such as sample plates 306 e.g., quant plates, work plates, etc.), consumable carriers 308 e.g., carrying disposable tips, etc.), etc., that may be needed for a library prep process and can be accessed in consumables bay 300A for use in assay bays 200 and / or transfer bay 400, as required. The consumables may be located inpredetermined locations on deck 302 or can be located in a vertically oriented storage unit 700, as described below.

[0108] In the implementation shown, vertically oriented storage unit 700 is configured to receive consumable carriers 308 and is positioned above deck 302 and is mounted to a top surface 304 of deck 302. In alternative implementations, rather than being mounted to top surface 304 of deck 302, vertically oriented storage unit 700 could also be mounted to movable wall 108A of cabinet 102 (see, e.g., Fig. 5). Vertically oriented storage unit 700 includes a plurality of horizontally extending shelves 702 that are each configured to receive a consumable carrier 308. In alternative implementations, vertically oriented storage unit 700 could also have a drawer positioned on each of the shelves 702, with each drawer configured to receive a consumable carrier 308 (see, e.g., Fig. 6). Storing consumable carriers 308 in vertically oriented storage unit 700 allows more consumable carriers 308 to be stored in consumables bay 300A without having to place consumable carriers side-by-side, thus reducing the footprint e.g., the XY dimensions) of consumables bay 300A.

[0109] To load consumable carriers 308 onto shelves 702, a front side of vertically oriented storage unit 700 e.g., the side facing movable wall 108A of cabinet 102) can have movable doors 706. Each movable door 706 can be aligned with a shelf space 704 above one of the shelves 702 and can allow a user to load consumable carriers 308 onto shelves 702 through doors 706. Doors 706 can be hingedly connected to a frame of vertically oriented storage unit 700 to allow doors 706 to be opened horizontally or vertically. In an alternate implementation, rather than having doors 706, the front side of vertically oriented storage unit 700 could be open such that consumable carriers 308 can be placed directly onto shelves 702. Instead of, or in addition to, having doors 706 on vertically oriented storage unit 700 to load consumable carriers 308 onto shelves 702, movable wall 108A could include doors 128 that are each aligned with a shelf space 704 {see, e.g., Fig. 4) to allow a user to load consumable carriers 308 onto shelves 702 through doors 128 without having to open movable wall 108A of cabinet 102.

[0110] To access and move consumable carriers 308 located within vertically oriented storage unit 700, a gripper assembly 750A is located within cabinet 102 and is configured to move consumable carriers 308 between the shelves 702 of vertically oriented storage unit 700 and a staging area 312 on top surface 304 of deck 302 of consumable bay 300A, where the consumable carrier 308 can then be accessed for use, for example, by vertically oriented gripping apparatus 126 and / or pipettor 124 on cross-bay gantry 122. In the implementation shown, gripper assembly 750 is mounted to deck 302 of consumables bay 300A and has a horizontally oriented gripping apparatus 752A that is configured to approach / engage consumable carriers 308 from a side 310 of consumable carrier 308, rather than from the top. Horizontally oriented gripping apparatus 752A can be movably mounted to a vertical post 754 such that horizontally oriented gripping apparatus 752A can be moved in the Z direction. In addition, vertical post 754 can be movably mounted to a horizontal track 756, such that vertical post 754 and horizontally oriented gripping apparatus 752A can be moved in the Y direction. The YZ movement of horizontally oriented gripping apparatus 752A allows gripper assembly 750A to access consumable carriers 308 in vertically oriented storage unit 700 and move consumable carriers 308 between shelves 702 of vertically oriented storage unit 700 and staging area 312. In an alternative implementation, rather than having a gripper assembly 750A that is mounted to deck 302 of consumables bay 300A, apparatus 100A could have a gripper assembly 750B with a horizontally oriented gripping apparatus 752B that is mounted on cross-bay gantry 122 (see, e.g., Fig. 6).

[0111] Referring to Fig. 4, a second implementation of consumables bay 300B is illustrated in apparatus 100A, which can be used to reduce the footprint of apparatus 100A. In alternative embodiments, the structure described herein for use in consumables bay 300B can also be used in assay bay 200 and / or transfer bay 400.

[0112] Consumables bay 300B includes deck 302 that is positioned on base 104 of cabinet 102 and can be positioned adjacent a first side of the plurality of assay bays 200. Consumables bay 300B can be bulk loaded with and store consumables, preferably noncontamination risk consumables, such as sample plates 306 e.g., quant plates, work plates,etc.), consumable carriers 308 e.g., carrying disposable tips, etc.), etc., that may be needed for a library prep process and can be accessed in consumables bay 300B for use in assay bays 200 and / or transfer bay 400, as required. The consumables may be located in predetermined locations on deck 302 or can be located in a vertically oriented storage unit 700, as described below.

[0113] In the implementation shown, vertically oriented storage unit 700 is configured to receive consumable carriers 308 and is positioned above deck 302 and is mounted to a top surface 304 of deck 302. In alternative implementations, rather than being mounted to top surface 304 of deck 302, vertically oriented storage unit 700 could also be mounted to movable wall 108A of cabinet 102 (see, e.g., Fig. 5). Vertically oriented storage unit 700 includes a plurality of horizontally extending shelves 702 that are each configured to receive a consumable carrier 308. In alternative implementations, vertically oriented storage unit 700 could also have a drawer positioned on each of the shelves 702, with each drawer configured to receive a consumable carrier 308 (see, e.g., Fig. 6). Storing consumable carriers 308 in vertically oriented storage unit 700 allows more consumable carriers 308 to be stored in consumables bay 300B without having to place consumable carriers side-by-side, thus reducing the footprint e.g., the XY dimensions) of consumables bay 300B.

[0114] To load consumable carriers 308 onto shelves 702, the front side of vertically oriented storage unit 700 is open and movable wall 108A includes doors 128 that are each aligned with a shelf space 704 above a shelf 702 to allow a user to load consumable carriers 308 onto shelves 702 through doors 128 without having to open movable wall 108A of cabinet 102. In alternative implementations, in addition to doors 128 in movable wall 108A, the front side of vertically oriented storage unit 700 can also have movable doors 706, each aligned with a shelf space 704 above one of the shelves 702. Doors 706 can be hingedly connected to a frame of vertically oriented storage unit 700 to allow doors 706 to be opened horizontally or vertically.

[0115] To access and move consumable carriers 308 located within vertically oriented storage unit 700, a gripper assembly 750A is located within cabinet 102 and is configured tomove consumable carriers 308 between shelves 702 of vertically oriented storage unit 700 and staging area 312 on top surface 304 of deck 302 of consumable bay 300B, where the consumable carrier 308 can then be accessed for use, for example, by vertically oriented gripping apparatus 126 and / or pipettor 124 on cross-bay gantry 122. In the implementation shown, gripper assembly 750 is mounted to deck 302 of consumables bay 300B and has a horizontally oriented gripping apparatus 752A that is configured to approach / engage consumable carriers 308 from a side 310 of consumable carrier 308, rather than from the top. Horizontally oriented gripping apparatus 752A can be movably mounted to vertical post 754 such that horizontally oriented gripping apparatus 752A can be moved in the Z direction. In addition, vertical post 754 can be movably mounted to horizontal track 756, such that vertical post 754 and horizontally oriented gripping apparatus 752A can be moved in the Y direction. The YZ movement of horizontally oriented gripping apparatus 752A allows gripper assembly 750A to access consumable carriers 308 in vertically oriented storage unit 700 and move consumable carriers 308 between shelves 702 of vertically oriented storage unit 700 and staging area 312. In an alternative implementation, rather than having a gripper assembly 750A that is mounted to deck 302 of consumables bay 300A, apparatus 100A could have a gripper assembly 750B with a horizontally oriented gripping apparatus 752B that is mounted on cross-bay gantry 122 (see, e.g., Fig. 6).

[0116] Referring to Fig. 5, a third implementation of consumables bay 300C is illustrated in apparatus 100A, which can be used to reduce the footprint of apparatus 100A. In alternative embodiments, the structure described herein for use in consumables bay 300C can also be used in assay bay 200 and / or transfer bay 400.

[0117] Consumables bay 300C includes deck 302 that is positioned on base 104 of cabinet 102 and can be positioned adjacent a first side of the plurality of assay bays 200. Consumables bay 300C can be bulk loaded with and store consumables, preferably noncontamination risk consumables, such as sample plates 306 e.g., quant plates, work plates, etc.), consumable carriers 308 e.g., carrying disposable tips, etc.), etc., that may be needed for a library prep process and can be accessed in consumables bay 300B for use in assaybays 200 and / or transfer bay 400, as required. The consumables may be located in predetermined locations on deck 302 or can be located in a vertically oriented storage unit 700, as described below.

[0118] In the implementation shown, vertically oriented storage unit 700 is configured to receive consumable carriers 308 and is mounted to movable wall 108A of cabinet 102. In alternative implementations, vertically oriented storage unit 700 can be positioned above deck 302 and mounted to a top surface 304 of deck 302. Vertically oriented storage unit 700 includes a plurality of horizontally extending shelves 702 that are each configured to receive a consumable carrier 308. In alternative implementations, vertically oriented storage unit 700 could also have a drawer positioned on each of the shelves 702, with each drawer configured to receive a consumable carrier 308 (see, e.g., Fig. 6). Storing consumable carriers 308 in vertically oriented storage unit 700 allows more consumable carriers 308 to be stored in consumables bay 300C without having to place consumable carriers side-by-side, thus reducing the footprint e.g., the XY dimensions) of consumables bay 300C.

[0119] To load consumable carriers 308 onto shelves 702, the front side of vertically oriented storage unit 700 is open and movable wall 108A includes doors 128 that are each aligned with a shelf space 704 above a shelf 702 to allow a user to load consumable carriers 308 onto shelves 702 through doors 128 without having to open movable wall 108A of cabinet 102. In addition, movable wall 108A could be opened and consumable carriers 308 could be loaded onto shelves 702 via a rear side of vertically oriented storage unit 700.

[0120] To access and move consumable carriers 308 located within vertically oriented storage unit 700, gripper assembly 750A is located within cabinet 102 and is configured to move consumable carriers 308 between shelves 702 of vertically oriented storage unit 700 and staging area 312 on top surface 304 of deck 302 of consumable bay 300C, where the consumable carrier 308 can then be accessed for use, for example, by vertically oriented gripping apparatus 126 and / or pipettor 124 on cross-bay gantry 122. In the implementation shown, gripper assembly 750 is mounted to deck 302 of consumables bay 300C and has a horizontally oriented gripping apparatus 752A that is configured to approach / engageconsumable carriers 308 from a side 310 of consumable carrier 308, rather than from the top. Horizontally oriented gripping apparatus 752A can be movably mounted to vertical post 754 such that horizontally oriented gripping apparatus 752A can be moved in the Z direction. In addition, vertical post 754 can be movably mounted to horizontal track 756, such that vertical post 754 and horizontally oriented gripping apparatus 752A can be moved in the Y direction. The YZ movement of horizontally oriented gripping apparatus 752A allows gripper assembly 750A to access consumable carriers 308 in vertically oriented storage unit 700 and move consumable carriers 308 between shelves 702 of vertically oriented storage unit 700 and staging area 312. In an alternative implementation, rather than having a gripper assembly 750A that is mounted to deck 302 of consumables bay 300A, apparatus 100A could have a gripper assembly 750B with a horizontally oriented gripping apparatus 752B that is mounted on cross-bay gantry 122 (see, e.g., Fig. 6).

[0121] Referring to Fig. 6, a fourth implementation of consumables bay 300D is illustrated in apparatus 100A, which can be used to reduce the footprint of apparatus 100A. In alternative embodiments, the structure described herein for use in consumables bay 300D can also be used in assay bay 200 and / or transfer bay 400.

[0122] Consumables bay 300D includes deck 302 that is positioned on base 104 of cabinet 102 and can be positioned adjacent a first side of the plurality of assay bays 200. Consumables bay 300D can be bulk loaded with and store consumables, preferably noncontamination risk consumables, such as sample plates 306 e.g., quant plates, work plates, etc.), consumable carriers 308 e.g., carrying disposable tips, etc.), etc., that may be needed for a library prep process and can be accessed in consumables bay 300D for use in assay bays 200 and / or transfer bay 400, as required. The consumables may be located in predetermined locations on deck 302 or can be located in a vertically oriented storage unit 700, as described below.

[0123] In the implementation shown, vertically oriented storage unit 700 is configured to receive consumable carriers 308 and is positioned above deck 302 and is mounted to a top surface 304 of deck 302. In alternative implementations, rather than being mounted to topsurface 304 of deck 302, vertically oriented storage unit 700 could also be mounted to movable wall 108A of cabinet 102 (see, e.g., Fig. 5). Vertically oriented storage unit 700 includes horizontally extending shelves 702 and a drawer 708, configured to receive a consumable carrier 308, positioned on each shelf 702. Storing consumable carriers 308 in vertically oriented storage unit 700 allows more consumable carriers 308 to be stored in consumables bay 300D without having to place consumable carriers side-by-side, thus reducing the footprint e.g., the XY dimensions) of consumables bay 300D.

[0124] To load consumable carriers 308 into drawers 708, the front side of vertically oriented storage unit 700 is open and movable wall 108A includes doors 128 that are each aligned with a drawer 708 to allow a user to pull a drawer 708 through a door 128 and load consumable carriers 308 into the drawer 708 without having to open movable wall 108A of cabinet 102. In addition, movable wall 108A could be opened and consumable carriers 308 could be loaded into drawers 708 via a rear side of vertically oriented storage unit 700.

[0125] To access and move consumable carriers 308 located within drawers 708 of vertically oriented storage unit 700, a gripper assembly 750B is located within cabinet 102 and is configured to move consumable carriers 308 between drawers 708 of vertically oriented storage unit 700 and staging area 312 on top surface 304 of deck 302 of consumable bay 300D, where the consumable carrier 308 can then be accessed for use, for example, by vertically oriented gripping apparatus 126 and / or pipettor 124 on cross-bay gantry 122. In the implementation shown, gripper assembly 750B includes a horizontally oriented gripping apparatus 752B that is mounted on cross-bay gantry 122, in addition to pipettor 124 and vertically oriented gripping apparatus 126. The YZ movement of horizontally oriented gripping apparatus 752B and vertically oriented gripping apparatus 126 on cross-bay gantry 122 allows gripper assembly 750B and vertically oriented gripping apparatus 126 to access consumable carriers 308 in drawers 708 of vertically oriented storage unit 700 and move consumable carriers 308 between drawers 708 and staging area 312. In an alternative implementation, rather than having gripper assembly 750B on cross-bay gantry 122, gripper assembly 750A can mounted to deck 302 of consumables bay 300D with horizontally oriented grippingapparatus 752A (see, e.g., Fig. 3). Horizontally oriented gripping apparatus 752A can be movably mounted to vertical post 754 such that horizontally oriented gripping apparatus 752A can be moved in the Z direction. In addition, vertical post 754 can be movably mounted to horizontal track 756, such that vertical post 754 and horizontally oriented gripping apparatus 752A can be moved in the Y direction.

[0126] Referring to Fig. 7, a fifth implementation of consumables bay 300E is illustrated in apparatus 100A, which can be used to reduce the footprint of apparatus 100A. In alternative embodiments, the structure described herein for use in consumables bay 300E can also be used in assay bay 200 and / or transfer bay 400.

[0127] Consumables bay 300E includes a deck 302 that is positioned on base 104 of cabinet 102 and can be positioned adjacent a first side of the plurality of assay bays 200. Consumables bay 300E can be bulk loaded with and store consumables, preferably noncontamination risk consumables, such as sample plates 306 (e.g., quant plates, work plates, etc.), consumable carriers 308 (e.g., carrying disposable tips, etc.), etc., that may be needed for a library prep process and can be accessed in consumables bay 300E for use in assay bays 200 and / or transfer bay 400, as required.

[0128] In the implementation shown, consumable carriers 308 are stacked in a vertical stack 720 that is positioned on top surface 304 of deck 302. Storing consumable carriers 308 in vertical stack 720 allows more consumable carriers 308 to be stored in consumables bay 300E without having to place consumable carriers side-by-side, thus reducing the footprint (e.g., the XY dimensions) of consumables bay 300E.

[0129] To access and move consumable carriers 308 located vertical stack 720, gripper assembly 750A is located within cabinet 102 and is configured to move consumable carriers 308 from vertical stack 720 to staging area 312 on top surface 304 of deck 302 of consumable bay 300E, where the consumable carrier 308 can then be accessed for use, for example, by vertically oriented gripping apparatus 126 and / or pipettor 124 on cross-bay gantry 122. Gripper assembly 750A can also be configured to move consumable carriers 308 from staging area 312 to a discard area 314 or discard container when a new consumable carrier 308 isneeded. In the implementation shown, gripper assembly 750A is mounted to deck 302 of consumables bay 300E and has a horizontally oriented gripping apparatus 752A that is configured to approach / engage consumable carriers 308 from a side 310 of consumable carrier 308, rather than from the top. Horizontally oriented gripping apparatus 752A can be movably mounted to a vertical post 754 such that horizontally oriented gripping apparatus 752A can be moved in the Z direction. In addition, vertical post 754 can be movably mounted to a horizontal track 756, such that vertical post 754 and horizontally oriented gripping apparatus 752A can be moved in the Y direction. The YZ movement of horizontally oriented gripping apparatus 752A allows gripper assembly 750A to access consumable carriers 308 in vertical stack 720 and move consumable carriers 308 between vertical stack 720 and staging area 312 and between staging area 312 and discard area 314.

[0130] Referring to Fig. 8, a sixth implementation of consumables bay 300F is illustrated in apparatus 100A, which can be used to reduce the footprint of apparatus 100A. In alternative embodiments, the structure described herein for use in consumables bay 300F can also be used in assay bay 200 and / or transfer bay 400.

[0131] Consumables bay 300F includes a deck 302 that is positioned on base 104 of cabinet 102 and can be positioned adjacent a first side of the plurality of assay bays 200. Consumables bay 300F can be bulk loaded with and store consumables, preferably noncontamination risk consumables, such as sample plates 306 (e.g., quant plates, work plates, etc.), consumable carriers 308 e.g., carrying disposable tips, etc.), etc., that may be needed for a library prep process and can be accessed in consumables bay 300F for use in assay bays 200 and / or transfer bay 400, as required.

[0132] In the implementation shown, consumable carriers 308 are stacked in a vertical stack 720 that is positioned on top surface 304 of deck 302. Storing consumable carriers 308 in vertical stack 720 allows more consumable carriers 308 to be stored in consumables bay 300F without having to place consumable carriers side-by-side, thus reducing the footprint e.g., the XY dimensions) of consumables bay 300F.

[0133] To access and move consumable carriers 308 located in vertical stack 720, gripper assembly 750B is located within cabinet 102 and is configured to move consumable carriers 308 from vertical stack 720 to staging area 312 on top surface 304 of deck 302 of consumable bay 300F, where the consumable carrier 308 can then be accessed for use, for example, by vertically oriented gripping apparatus 126 and / or pipettor 124 on cross-bay gantry 122. Gripper assembly 750B can also be configured to move consumable carriers 308 from staging area 312 to a discard area 314 or discard container when a new consumable carrier 308 is needed. In the implementation shown, gripper assembly 750B includes a horizontally oriented gripping apparatus 752B that is mounted on cross-bay gantry 122, in addition to pipettor 124 and vertically oriented gripping apparatus 126. Horizontally oriented gripping apparatus 752B is configured to approach / engage consumable carriers 308 from a side 310 of consumable carrier 308, rather than from the top.

[0134] Referring to Fig. 9, a second implementation of an apparatus 100B is illustrated that can be used to implement system 500. Apparatus 100B is the same as apparatus 100A described above, except that apparatus 100B includes at least one consumables bay 800, rather than at least one consumables bay 300.

[0135] Referring to Fig. 10, a first implementation of consumables bay 800A is illustrated in apparatus 100B, which can be used to reduce the footprint of apparatus 100B. In alternative embodiments, the structure described herein for use in consumables bay 800A can also be used in assay bay 200 and / or transfer bay 400.

[0136] Consumables bay 800A includes a deck 802 that is positioned on base 104 of cabinet 102 and can be positioned adjacent a first side of the plurality of assay bays 200. In the implementation shown, consumables bay 800A also includes a movable drawer 816 that is movably mounted to deck 802 and is movable between a closed position and an open position. In the open position, movable drawer 816 can be bulk loaded with and store consumables, preferably non-contamination risk consumables, such as sample plates 806 (e.g., quant plates, work plates, etc.), consumable carriers 808 e.g., carrying disposable tips, etc.), etc., that may be needed for a library prep process and can be accessed in consumablesbay 800A for use in assay bays 200 and / or transfer bay 400, as required. The consumables may be located in predetermined locations on a bottom 818 of movable drawer 816 or can be located in a vertically oriented storage unit 700, as described below.

[0137] In the implementation shown, vertically oriented storage unit 700 is configured to receive consumable carriers 808 and is configured such that portions of vertically oriented storage unit 700 can move between positions above deck 802 and below deck 802 and within movable drawer 816 via a lift mechanism 900 that is operatively connected to vertically oriented storage unit 700. Vertically oriented storage unit 700 includes a plurality of horizontally extending shelves 702 that are each configured to receive a consumable carrier 808. In alternative implementations, vertically oriented storage unit 700 could also have a drawer 708 positioned on each of the shelves 702, with each drawer configured to receive a consumable carrier 808 (see, e.g., Fig. 6). Storing consumable carriers 808 in vertically oriented storage unit 700 allows more consumable carriers 808 to be stored in consumables bay 800A without having to place consumable carriers side-by-side, thus reducing the footprint e.g., the XY dimensions) of consumables bay 800A.

[0138] To load consumable carriers 808 onto shelves 702, a front side of vertically oriented storage unit 700 e.g., the side facing movable wall 108A of cabinet 102) can have movable doors 706. Each movable door 706 can be aligned with a shelf space 704 above one of the shelves 702 and can allow a user to load consumable carriers 808 onto shelves 702 through doors 706. Doors 706 can be hingedly connected to a frame of vertically oriented storage unit 700 to allow doors 706 to be opened horizontally or vertically. In an alternate implementation, rather than having doors 706, the front side of vertically oriented storage unit 700 could be open such that consumable carriers 308 can be placed directly onto shelves 702.

[0139] To access and move consumable carriers 808 located within vertically oriented storage unit 700, gripper assembly 750A can be located within cabinet 102 and configured to move consumable carriers 808 between the shelves 702 of vertically oriented storage unit 700 and a staging area 822 on a top surface 820 of bottom 818 of movable drawer 816, where theconsumable carrier 808 can then be accessed for use, for example, by vertically oriented gripping apparatus 126 and / or pipettor 124 on cross-bay gantry 122. In the implementation shown, gripper assembly 750A is mounted to deck 802 of consumables bay 800A and has a horizontally oriented gripping apparatus 752A that is configured to approach / engage consumable carriers 808 from a side 810 of consumable carrier 808, rather than from the top. Horizontally oriented gripping apparatus 752A can be movably mounted to vertical post 754 such that horizontally oriented gripping apparatus 752A can be moved in the Z direction. In addition, vertical post 754 can be movably mounted to horizontal track 756, such that vertical post 754 and horizontally oriented gripping apparatus 752A can be moved in the Y direction. The YZ movement of horizontally oriented gripping apparatus 752A allows gripper assembly 750A to access consumable carriers 808 in vertically oriented storage unit 700 and move consumable carriers 808 between shelves 702 of vertically oriented storage unit 700 and staging area 822. As consumable carriers 808 are removed or replaced in vertically oriented storage unit 700, vertically oriented storage unit 700 can be moved vertically upward or downward by lift mechanism 900 to make more or less of the consumable carriers 808 accessible to gripper assembly 750A.

[0140] Referring to Fig. 1 1 , a second implementation of consumables bay 800B is illustrated in apparatus 100B, which can be used to reduce the footprint of apparatus 100B. In alternative embodiments, the structure described herein for use in consumables bay 800B can also be used in assay bay 200 and / or transfer bay 400.

[0141] Consumables bay 800B includes deck 802 that is positioned on base 104 of cabinet 102 and can be positioned adjacent a first side of the plurality of assay bays 200. In the implementation shown, consumables bay 800B also includes movable drawer 816 that is movably mounted to deck 802 and is movable between a closed position and an open position. In the open position, movable drawer 816 can be bulk loaded with and store consumables, preferably non-contamination risk consumables, such as sample plates 806 (e.g., quant plates, work plates, etc.), consumable carriers 808 e.g., carrying disposable tips, etc.), etc., that may be needed for a library prep process and can be accessed in consumables bay 800Bfor use in assay bays 200 and / or transfer bay 400, as required. The consumables may be located in predetermined locations on a bottom 818 of movable drawer 816 or can be located in a vertically oriented storage unit 700, as described below.

[0142] In the implementation shown, vertically oriented storage unit 700 is configured to receive consumable carriers 808 and is configured such that portions of vertically oriented storage unit 700 can move between positions above deck 802 and below deck 802 and within movable drawer 816 via a lift mechanism 900 that is operatively connected to vertically oriented storage unit 700. Vertically oriented storage unit 700 includes a plurality of horizontally extending shelves 702 that are each configured to receive a consumable carrier 808. In alternative implementations, vertically oriented storage unit 700 could also have a drawer 708 positioned on each of the shelves 702, with each drawer 708 configured to receive a consumable carrier 808 (see, e.g., Fig. 6). Storing consumable carriers 808 in vertically oriented storage unit 700 allows more consumable carriers 808 to be stored in consumables bay 800B without having to place consumable carriers side-by-side, thus reducing the footprint e.g., the XY dimensions) of consumables bay 800B.

[0143] To load consumable carriers 808 onto shelves 702, a front side of vertically oriented storage unit 700 e.g., the side facing movable wall 108A of cabinet 102) can have movable doors 706. Each movable door 706 can be aligned with a shelf space 704 above one of the shelves 702 and can allow a user to load consumable carriers 808 onto shelves 702 through doors 706. Doors 706 can be hingedly connected to a frame of vertically oriented storage unit 700 to allow doors 706 to be opened horizontally or vertically. In an alternate implementation, rather than having doors 706, the front side of vertically oriented storage unit 700 could be open such that consumable carriers 308 can be placed directly onto shelves 702.

[0144] To access and move consumable carriers 808 located within vertically oriented storage unit 700, gripper assembly 750B can be located within cabinet 102 and configured to move consumable carriers 808 between the shelves 702 of vertically oriented storage unit 700 and a staging area 822 on a top surface 820 of bottom 818 of movable drawer 816, where theconsumable carrier 808 can then be accessed for use, for example, by vertically oriented gripping apparatus 126 and / or pipettor 124 on cross-bay gantry 122. In the implementation shown, gripper assembly 750B includes a horizontally oriented gripping apparatus 752B that is mounted on cross-bay gantry 122, in addition to pipettor 124 and vertically oriented gripping apparatus 126. Horizontally oriented gripping apparatus 752B is configured to approach / engage consumable carriers 808 from a side 810 of consumable carrier 808, rather than from the top. The YZ movement of horizontally oriented gripping apparatus 752B allows gripper assembly 750B to access consumable carriers 808 in vertically oriented storage unit 700 and move consumable carriers 808 between shelves 702 of vertically oriented storage unit 700 and staging area 822. As consumable carriers 808 are removed or replaced in vertically oriented storage unit 700, vertically oriented storage unit 700 can be moved vertically upward or downward by lift mechanism 900 to make more or less of the consumable carriers 808 accessible to gripper assembly 750B.

[0145] Referring to Fig. 12, a first implementation of a method 1000 for reducing the footprint of a library preparation system (e.g., system 500) using apparatus 100A discussed above is illustrated.

[0146] At Step 1005 of method 100, a plurality of consumable carriers e.g., consumable carriers 308) are received in a vertically oriented storage unit e.g., vertically oriented storage unit 700) that is positioned above a deck {e.g., deck 302) of a consumables bay {e.g., consumables bay 300A, 300B, 300C, 300D), which are positioned within a working chamber {e.g., working chamber 110) that is defined and enclosed by a cabinet {e.g., cabinet 102). The vertically oriented storage unit can have horizontally extending shelves {e.g., shelves 702) and, in some implementations, can have drawers {e.g., drawers 708) positioned on the shelves and the consumable carriers are received on the shelves or in the drawers of the vertically oriented storage unit. The consumable carriers can be loaded directly onto the shelves or into the drawers via a movable wall {e.g., movable wall 108A) of the cabinet, via movable doors {e.g., movable doors 706) in the vertically oriented storage unit, or via movable doors {e.g., movable doors 128) in the movable wall of the cabinet.

[0147] At Step 1010, a nucleic acid library is prepared for sequencing in an assay bay (e.g., assay bay 200) that is positioned within the working chamber of the cabinet.

[0148] At Step 1015, one of the consumable carriers is removed from the vertically oriented storage unit using a gripper assembly e.g., gripper assembly 750A, 750B) located within the cabinet. The gripper assembly can be a standalone gripper assembly e.g., gripper assembly 750A) or a gripper assembly mounted to a cross-bay gantry {e.g., gripper assembly 750B mounted to cross-bay gantry 122).

[0149] At Step 1020, the consumable carrier removed from the vertically oriented storage unit is placed onto a staging area {e.g., staging area 312) on the deck of the consumables bay using the gripper assembly. In some implementations, the consumable carrier placed in the staging area can also be moved from the staging area back to the vertically oriented storage unit using the gripping assembly, when required.

[0150] Referring to Fig. 13, a second implementation of a method 1100 for reducing the footprint of a library preparation system {e.g., system 500) using apparatus 100A discussed above is illustrated.

[0151] At Step 1105 of method 1100, a vertical stack {e.g., stack 720) of consumable carriers {e.g., consumable carriers 308) is received on a top surface {e.g., top surface 304) of a deck {e.g., deck 302) of a consumables bay {e.g., consumable bay 300E, 300F), which is positioned within a working chamber {e.g., working chamber 110) defined and enclosed by a cabinet {e.g., cabinet 102).

[0152] At Step 1110, a nucleic acid library is prepared for sequencing in an assay bay {e.g., assay bay 200) positioned with the working chamber of the cabinet.

[0153] At Step 1115, one of the consumable carriers is engaged from a side of the consumable carrier and removed from the vertical stack using a gripper assembly {e.g., gripper assembly 750A, 750B) located within the cabinet. The gripper assembly includes a horizontally oriented gripping apparatus {e.g., horizontally oriented gripping apparatus 752A, 752B) and can be a standalone gripper assembly {e.g., gripper assembly 750A) mounted tothe deck of the consumables bay or a gripper assembly {e.g., gripper assembly 750B) mounted on a cross-bay gantry e.g., cross-bay gantry 122).

[0154] At Step 1120, the consumable carrier removed from the vertical stack is placed onto a staging area e.g., staging area 312) on the deck of the consumables bay using the gripper assembly. In some implementations, the consumable carrier placed in the staging area can also be moved from the staging area to a discard area {e.g., discard area 314) or discard container using the gripping assembly, when required.

[0155] Referring to Fig. 14, a third implementation of a method 1200 for reducing the footprint of a library preparation system (e.g., system 500) using the apparatus 100B discussed above is illustrated.

[0156] At Step 1205 of method 1200, a plurality of consumable carriers {e.g., consumable carriers 808) are received in a vertically oriented storage unit {e.g., vertically oriented storage unit 700) that is configured to move between positions above a deck {e.g., deck 802) of a consumables bay {e.g., consumables bay 800A, 800B) and positions below the deck and within a movable drawer {e.g., drawer 816) of the consumables bay via a lift mechanism {e.g., lift mechanism 900). The consumables bay is positioned within a working chamber {e.g., working chamber 110) defined and enclosed by a cabinet {e.g., cabinet 102). The vertically oriented storage unit can have horizontally extending shelves {e.g., shelves 702) and, in some implementations, can have drawers {e.g., drawers 708) positioned on the shelves and the consumable carriers are received on the shelves or in the drawers of the vertically oriented storage unit. The consumable carriers can be loaded directly onto the shelves or into the drawers via a movable wall {e.g., movable wall 108A) of the cabinet or via movable doors {e.g., movable doors 706) in the vertically oriented storage unit.

[0157] At Step 1210, a nucleic acid library for sequencing is prepared in an assay bay (e.g., assay bay 200) positioned with the working chamber of the cabinet.

[0158] At Step 1215, one of the consumable carriers is removed from the vertically oriented storage unit using a gripper assembly {e.g., gripper assembly 750A, 750B) located within the cabinet. The gripper assembly can be a standalone gripper assembly {e.g., gripperassembly 750A) mounted to the deck of the consumables bay or a gripper assembly {e.g., gripper assembly 750B) with a horizontally oriented gripping apparatus e.g., horizontally oriented gripping apparatus 752B) mounted on cross-bay gantry e.g., cross-bay gantry 122).

[0159] Example 1

[0160] An apparatus comprising: a cabinet defining and enclosing a working chamber; an assay bay positioned within the working chamber of the cabinet, the assay bay configured to prepare a nucleic acid library for sequencing; a consumables bay positioned within the working chamber of the cabinet; a vertically oriented storage unit positioned above a deck of the consumables bay, the storage unit configured to receive a plurality of consumable carriers; and a gripper assembly located within the cabinet, the gripper assembly configured to move a consumable carrier of the plurality of consumable carriers between the vertically oriented storage unit and a staging area on a top surface of the deck of the consumables bay.

[0161] Example 2

[0162] The apparatus of example 1 , wherein the gripper assembly comprises a horizontally oriented gripping apparatus mounted on a cross-bay gantry positioned within the cabinet.

[0163] Example s

[0164] The apparatus of example 2, wherein the apparatus comprises a pipettor and a vertically oriented gripping apparatus mounted on the cross-bay gantry.

[0165] Example 4

[0166] The apparatus of any one of examples 1 -3, wherein the gripper assembly is mounted to the deck of the consumables bay.

[0167] Example s

[0168] The apparatus of any one of examples 1 -4, wherein the vertically oriented storage unit comprises a plurality of horizonal shelves, each shelf of the plurality of horizontal shelves configured to receive a consumable carrier of the plurality of consumable carriers.

[0169] Example s

[0170] The apparatus of any one of examples 1 -5, wherein the vertically oriented storage unit is mounted to the top surface of the deck of the consumables bay.

[0171] Example 7

[0172] The apparatus of any one of examples 1 -6, wherein the vertically oriented storage unit comprises a plurality of movable doors, each door aligned with a shelf space above one of the plurality of horizontal shelves.

[0173] Example s

[0174] The apparatus of any one of examples 1 -5, wherein the vertically oriented storage unit is mounted to a movable wall of the cabinet.

[0175] Example s

[0176] The apparatus of example 8, wherein the movable wall of the cabinet comprises a plurality of movable doors, each door aligned with a shelf space above one of the plurality of horizontal shelves.

[0177] Example 10

[0178] The apparatus of any one of example 1 -9, wherein the vertically oriented storage unit comprises a plurality of drawers, each of the drawers configured to receive a consumable carrier of the plurality of consumable carriers.

[0179] Example 1 1

[0180] The apparatus of example 10, wherein the vertically oriented storage unit is mounted to a top surface of the deck of the consumables bay.

[0181] Example 12

[0182] The apparatus of example 10, wherein the vertically oriented storage unit is mounted to a movable wall of the cabinet.

[0183] Example 13

[0184] The apparatus of example 12, wherein the movable wall of the cabinet comprises a plurality of movable doors, each door aligned with a drawer of the plurality of drawers.

[0185] Example 14

[0186] A method, comprising: receiving a plurality of consumable carriers in a vertically oriented storage unit positioned above a deck of a consumables bay, the consumables bay being positioned within a working chamber defined and enclosed by a cabinet; preparing a nucleic acid library for sequencing in an assay bay positioned with the working chamber of the cabinet; removing a consumable carrier of the plurality of consumable carriers from the storage unit using a gripper assembly located within the cabinet; and placing the consumable carrier removed from the storage unit onto a staging area on the deck of the consumables bay using the gripper assembly.

[0187] Example 15

[0188] The method of example 14, comprising removing the consumable carrier from the staging area and placing the consumable carrier into the storage unit.

[0189] Example 16

[0190] The method of any one of examples 14-15, wherein the gripper assembly comprises a horizontally oriented gripping apparatus mounted on a cross-bay gantry positioned within the cabinet.

[0191] Example 17

[0192] The method of example 16, wherein a pipettor and a vertically oriented gripping apparatus are mounted on the cross-bay gantry.

[0193] Example 18

[0194] The method of any one of examples 14-15, wherein the gripper assembly is mounted to the deck of the consumables bay.

[0195] Example 19

[0196] The method of any one of examples 14-18, comprising loading the plurality of consumable carriers onto a plurality of horizonal shelves of the vertically oriented storage unit.

[0197] Example 20

[0198] The method of any one of examples 14-19, comprising loading the plurality of consumable carriers onto the plurality of horizonal shelves via a plurality of movable doors in the vertically oriented storage unit.

[0199] Example 21

[0200] The method of any one of examples 14-19, comprising loading the plurality of consumable carriers onto the plurality of horizontal shelves via a plurality of movable doors in a movable wall of the cabinet.

[0201] Example 22

[0202] The method of any one of examples 14-18, comprising loading the plurality of consumable carriers into a plurality of drawers of the vertically oriented storage unit.

[0203] Example 23

[0204] The method of any one of examples 14-19, comprising loading the plurality of consumable carriers into the plurality of drawers via a plurality of movable doors in a movable wall of the cabinet.

[0205] Example 24

[0206] An apparatus, comprising: a cabinet defining and enclosing a working chamber; an assay bay positioned within the working chamber of the cabinet, the assay bay configured to prepare a nucleic acid library for sequencing; a consumables bay positioned within the working chamber of the cabinet; and a gripper assembly located within the cabinet, the gripper assembly comprising a horizontally oriented gripping apparatus and configured to: engage a consumable carrier located in a vertical stack of consumable carriers positioned on a top surface of a deck of the consumable bay from a side of the consumable carrier; and move the consumable carrier from the vertical stack of consumable carriers to a staging area located on the top surface of the deck.

[0207] Example 25

[0208] The apparatus of example 24, wherein the gripper assembly is configured to move the consumable carrier from the staging area to a discard area.

[0209] Example 26

[0210] The apparatus of any one of examples 24-25, wherein the horizontally oriented gripping apparatus is mounted on a cross-bay gantry positioned within the cabinet.

[0211] Example 27

[0212] The apparatus of example 26, wherein the apparatus comprises a pipettor and a vertically oriented gripping apparatus mounted on the cross-bay gantry.

[0213] Example 28

[0214] The apparatus of any one of examples 24-25, wherein the gripper assembly is mounted to the deck of the consumables bay.

[0215] Example 29

[0216] A method, comprising: receiving a vertical stack of consumable carriers on a top surface of a deck of a consumables bay, the consumables bay being positioned within a working chamber defined and enclosed by a cabinet; preparing a nucleic acid library for sequencing in an assay bay positioned with the working chamber of the cabinet; engaging a consumable carrier of the stack of consumable carriers from a side of the consumable carrier and removing the consumable carrier from the vertical stack of consumable carriers using a gripper assembly located within the cabinet, the gripper assembly comprising a horizontally oriented gripping apparatus; and placing the consumable carrier removed from the vertical stack of consumable carriers onto a staging area on the deck of the consumables bay using the gripper assembly.

[0217] Example 30

[0218] The method of example 29, comprising removing the consumable carrier from the staging area and placing the consumable carrier in a discard area using the gripper assembly.

[0219] Example 31

[0220] The method of any one of examples 29-30, wherein the horizontally oriented gripping apparatus is mounted on a cross-bay gantry positioned within the cabinet.

[0221] Example 32

[0222] The method of example 31 , wherein a pipettor and a vertically oriented gripping apparatus are mounted on the cross-bay gantry.

[0223] Example 33

[0224] The method of any one of examples 29-30, wherein the gripper assembly is mounted to the deck of the consumables bay.

[0225] Example 34

[0226] An apparatus, comprising: a cabinet defining and enclosing a working chamber; an assay bay positioned within the working chamber of the cabinet, the assay bay configured to prepare a nucleic acid library for sequencing; a consumables bay positioned within the working chamber of the cabinet, the consumables bay comprising a deck and a movable drawer; a vertically oriented storage unit configured to receive a plurality of consumable carriers and to move between positions above the deck of the consumable bay and positions below the deck and within the movable drawer; and a gripper assembly located within the cabinet, the gripper assembly configured to move a consumable carrier of the plurality of consumable carriers between the vertically oriented storage unit and a staging area on a top surface of a bottom of the movable drawer.

[0227] Example 35

[0228] The apparatus of example 34, comprising a lift mechanism operatively connected to the vertically oriented storage unit and configured to move the vertically oriented storage unit between the positions above the deck and positions below the deck and within the movable drawer.

[0229] Example 36

[0230] The apparatus of any one of examples 34-35, wherein the gripper assembly comprises a horizontally oriented gripping apparatus mounted on a cross-bay gantry positioned within the cabinet.

[0231] Example 37

[0232] The apparatus of example 36, wherein the apparatus comprises a pipettor and a vertically oriented gripping apparatus mounted on the cross-bay gantry.

[0233] Example 38

[0234] The apparatus of any one of examples 34-35, wherein the gripper assembly is mounted to the deck of the consumables bay.

[0235] Example 39

[0236] The apparatus of any one of examples 34-38, wherein the vertically oriented storage unit comprises a plurality of horizonal shelves, each shelf of the plurality of horizontal shelves configured to receive a consumable carrier of the plurality of consumable carriers.

[0237] Example 40

[0238] The apparatus of example 39, wherein the vertically oriented storage unit comprises a plurality of movable doors, each door aligned with a shelf space above one of the plurality of horizontal shelves.

[0239] Example 41

[0240] The apparatus of any one of examples 34-38, wherein the vertically oriented storage unit comprises a plurality of drawers, each of the drawers configured to receive a consumable carrier of the plurality of consumable carriers.

[0241] Example 42

[0242] A method, comprising: receiving a plurality of consumable carriers in a vertically oriented storage unit configured to move between positions above a deck of a consumables bay and positions below the deck and within a movable drawer of the consumables bay, the consumables bay being positioned within a working chamber defined and enclosed by a cabinet; preparing a nucleic acid library for sequencing in an assay bay positioned with the working chamber of the cabinet; removing a consumable carrier of the plurality of consumable carriers from the storage unit using a gripper assembly located within the cabinet; and placing the consumable carrier removed from the storage unit onto a staging area on a top surface of a bottom of the movable drawer using the gripper assembly.

[0243] Example 43

[0244] The method of example 42, comprising removing the consumable carrier from the staging area and placing the consumable carrier into the storage unit.

[0245] Example 44

[0246] The method of any one of examples 42-43, wherein the gripper assembly comprises a horizontally oriented gripping apparatus mounted on a cross-bay gantry positioned within the cabinet.

[0247] Example 45

[0248] The method of example 44, wherein a pipettor and a vertically oriented gripping apparatus are mounted on the cross-bay gantry.

[0249] Example 46

[0250] The method of any one of examples 42-43, wherein the gripper assembly is mounted to the deck of the consumables bay.

[0251] Example 47

[0252] The method of any one of examples 42-46, comprising loading the plurality of consumable carriers onto a plurality of horizonal shelves of the vertically oriented storage unit.

[0253] Example 48

[0254] The method of example 47, comprising loading the plurality of consumable carriers onto the plurality of horizonal shelves via a plurality of movable doors in the vertically oriented storage unit.

[0255] Example 49

[0256] The method of any one of claims 42-46, comprising loading the plurality of consumable carriers into a plurality of drawers of the vertically oriented storage unit.

[0257] The foregoing description is provided to enable a person skilled in the art to practice the various configurations described herein. While the subject technology has been particularly described with reference to the various figures and configurations, it should be understood that these are for illustration purposes only and should not be taken as limiting the scope of the subject technology.

[0258] As used herein, an element or step recited in the singular and proceeded with the word “a” or “an” should be understood as not excluding plural of said elements or steps, unless such exclusion is explicitly stated. Furthermore, references to “one implementation” are not intended to be interpreted as excluding the existence of additional implementations that also incorporate the recited features. Moreover, unless explicitly stated to the contrary, implementations “comprising,” “including,” or “having” an element or a plurality of elements having a particular property may include additional elements whether or not they have thatproperty. Moreover, the terms “comprising,” including,” having,” or the like are interchangeably used herein.

[0259] The terms “connect,” “connected,” “contact” “coupled” and / or the like are broadly defined herein to encompass a variety of divergent arrangements and assembly techniques. These arrangements and techniques include, but are not limited to: (1 ) the direct joining of one component and another component with no intervening components therebetween ( / .e., the components are in direct physical contact); and (2) the joining of one component and another component with one or more components therebetween, provided that the one component being “connected to” or “contacting” or “coupled to” the other component is somehow in operative communication (e.g., electrically, fluidly, physically, optically, etc.) with the other component (notwithstanding the presence of one or more additional components therebetween). It is to be understood that some components that are in direct physical contact with one another may or may not be in electrical contact and / or fluid contact with one another. Moreover, two components that are electrically connected, electrically coupled, optically connected, optically coupled, fluidly connected or fluidly coupled may or may not be in direct physical contact, and one or more other components may be positioned therebetween.

[0260] The terms “generally”, “substantially," "approximately," and “about” used throughout this Specification are used to describe and account for small fluctuations, such as due to variations in processing. For example, they can refer to less than or equal to ±5%, such as less than or equal to ±2%, such as less than or equal to ±1%, such as less than or equal to ±0.5%, such as less than or equal to ±0.2%, such as less than or equal to ±0.1%, such as less than or equal to ±0.05%.

[0261] There may be many other ways to implement the subject technology. Various functions and elements described herein may be partitioned differently from those shown without departing from the scope of the subject technology. Various modifications to these implementations may be readily apparent to those skilled in the art, and generic principles defined herein may be applied to other implementations. Thus, many changes and modifications may be made to the subject technology, by one having ordinary skill in the art,without departing from the scope of the subject technology. For instance, different numbers of a given module or unit may be employed, a different type or types of a given module or unit may be employed, a given module or unit may be added, or a given module or unit may be omitted.

[0262] Underlined and / or italicized headings and subheadings are used for convenience only, do not limit the subject technology, and are not referred to in connection with the interpretation of the description of the subject technology. All structural and functional equivalents to the elements of the various implementations described throughout this disclosure that are known or later come to be known to those of ordinary skill in the art are expressly incorporated herein by reference and intended to be encompassed by the subject technology. Moreover, nothing disclosed herein is intended to be dedicated to the public regardless of whether such disclosure is explicitly recited in the above description.

[0263] It should be appreciated that all combinations of the foregoing concepts and additional concepts discussed in greater detail below (provided such concepts are not mutually inconsistent) are contemplated as being part of the subject matter disclosed herein. In particular, all combinations of claimed subject matter appearing at the end of this disclosure are contemplated as being part of the subject matter disclosed herein.

Claims

CLAIMSWhat is claimed is:1 . An apparatus, comprising: a cabinet defining and enclosing a working chamber; an assay bay positioned within the working chamber of the cabinet, the assay bay configured to prepare a nucleic acid library for sequencing; a consumables bay positioned within the working chamber of the cabinet; a vertically oriented storage unit positioned above a deck of the consumables bay, the storage unit configured to receive a plurality of consumable carriers; and a gripper assembly located within the cabinet, the gripper assembly configured to move a consumable carrier of the plurality of consumable carriers between the vertically oriented storage unit and a staging area on a top surface of the deck of the consumables bay.

2. The apparatus of claim 1 , wherein the gripper assembly comprises a horizontally oriented gripping apparatus mounted on a cross-bay gantry positioned within the cabinet.

3. The apparatus of claim 2, wherein the apparatus comprises a pipettor and a vertically oriented gripping apparatus mounted on the cross-bay gantry.

4. The apparatus of any one of claims 1 -3, wherein the gripper assembly is mounted to the deck of the consumables bay.

5. The apparatus of any one of claims 1 -4, wherein the vertically oriented storage unit comprises a plurality of horizonal shelves, each shelf of the plurality of horizontal shelves configured to receive a consumable carrier of the plurality of consumable carriers.

6. The apparatus of claim 5, wherein the vertically oriented storage unit is mounted to the top surface of the deck of the consumables bay.

7. The apparatus of any one of claims 5-6, wherein the vertically oriented storage unit comprises a plurality of movable doors, each door aligned with a shelf space above one of the plurality of horizontal shelves.

8. The apparatus of claim 5, wherein the vertically oriented storage unit is mounted to a movable wall of the cabinet.

9. The apparatus of claim 8, wherein the movable wall of the cabinet comprises a plurality of movable doors, each door aligned with a shelf space above one of the plurality of horizontal shelves.

10. The apparatus of any one of claims 1 -4, wherein the vertically oriented storage unit comprises a plurality of drawers, each of the drawers configured to receive a consumable carrier of the plurality of consumable carriers.

11. The apparatus of claim 10, wherein the vertically oriented storage unit is mounted to a top surface of the deck of the consumables bay.

12. The apparatus of claim 10, wherein the vertically oriented storage unit is mounted to a movable wall of the cabinet.

13. The apparatus of claim 12, wherein the movable wall of the cabinet comprises a plurality of movable doors, each door aligned with a drawer of the plurality of drawers.

14. A method, comprising: receiving a plurality of consumable carriers in a vertically oriented storage unit positioned above a deck of a consumables bay, the consumables bay being positioned within a working chamber defined and enclosed by a cabinet; preparing a nucleic acid library for sequencing in an assay bay positioned with the working chamber of the cabinet; removing a consumable carrier of the plurality of consumable carriers from the storage unit using a gripper assembly located within the cabinet; and placing the consumable carrier removed from the storage unit onto a staging area on the deck of the consumables bay using the gripper assembly.

15. The method of claim 14, comprising removing the consumable carrier from the staging area and placing the consumable carrier into the storage unit.

16. The method of any one of claim 14-15, wherein the gripper assembly comprises a horizontally oriented gripping apparatus mounted on a cross-bay gantry positioned within the cabinet.

17. The method of claim 16, wherein a pipettor and a vertically oriented gripping apparatus are mounted on the cross-bay gantry.

18. The method of any one of claims 14-15, wherein the gripper assembly is mounted to the deck of the consumables bay.

19. The method of any one of claims 14-18, comprising loading the plurality of consumable carriers onto a plurality of horizonal shelves of the vertically oriented storage unit.

20. The method of claim 19, comprising loading the plurality of consumable carriers onto the plurality of horizonal shelves via a plurality of movable doors in the vertically oriented storage unit.21 . The method of claim 19, comprising loading the plurality of consumable carriers onto the plurality of horizontal shelves via a plurality of movable doors in a movable wall of the cabinet.

22. The method of any one of claims 14-18, comprising loading the plurality of consumable carriers into a plurality of drawers of the vertically oriented storage unit.

23. The method of claim 22, comprising loading the plurality of consumable carriers into the plurality of drawers via a plurality of movable doors in a movable wall of the cabinet.

24. An apparatus, comprising: a cabinet defining and enclosing a working chamber; an assay bay positioned within the working chamber of the cabinet, the assay bay configured to prepare a nucleic acid library for sequencing; a consumables bay positioned within the working chamber of the cabinet; and a gripper assembly located within the cabinet, the gripper assembly comprising a horizontally oriented gripping apparatus and configured to: engage a consumable carrier located in a vertical stack of consumable carriers positioned on a top surface of a deck of the consumable bay from a side of the consumable carrier; and move the consumable carrier from the vertical stack of consumable carriers to a staging area located on the top surface of the deck.

25. The apparatus of claim 24, wherein the gripper assembly is configured to move the consumable carrier from the staging area to a discard area.

26. The apparatus of any one of claims 24-25, wherein the horizontally oriented gripping apparatus is mounted on a cross-bay gantry positioned within the cabinet.

27. The apparatus of claim 26, wherein the apparatus comprises a pipettor and a vertically oriented gripping apparatus mounted on the cross-bay gantry.

28. The apparatus of claim 24, wherein the gripper assembly is mounted to the deck of the consumables bay.

29. A method, comprising: receiving a vertical stack of consumable carriers on a top surface of a deck of a consumables bay, the consumables bay being positioned within a working chamber defined and enclosed by a cabinet; preparing a nucleic acid library for sequencing in an assay bay positioned with the working chamber of the cabinet; engaging a consumable carrier of the stack of consumable carriers from a side of the consumable carrier and removing the consumable carrier from the vertical stack of consumable carriers using a gripper assembly located within the cabinet, the gripper assembly comprising a horizontally oriented gripping apparatus; and placing the consumable carrier removed from the vertical stack of consumable carriers onto a staging area on the deck of the consumables bay using the gripper assembly.

30. The method of claim 29, comprising removing the consumable carrier from the staging area and placing the consumable carrier in a discard area using the gripper assembly.

31. The method of any one of claims 29-30, wherein the horizontally oriented gripping apparatus is mounted on a cross-bay gantry positioned within the cabinet.

32. The method of claim 31 , wherein a pipettor and a vertically oriented gripping apparatus are mounted on the cross-bay gantry.

33. The method of claim 29, wherein the gripper assembly is mounted to the deck of the consumables bay.

34. An apparatus, comprising: a cabinet defining and enclosing a working chamber; an assay bay positioned within the working chamber of the cabinet, the assay bay configured to prepare a nucleic acid library for sequencing; a consumables bay positioned within the working chamber of the cabinet, the consumables bay comprising a deck and a movable drawer; a vertically oriented storage unit configured to receive a plurality of consumable carriers and to move between positions above the deck of the consumable bay and positions below the deck and within the movable drawer; and a gripper assembly located within the cabinet, the gripper assembly configured to move a consumable carrier of the plurality of consumable carriers between the vertically oriented storage unit and a staging area on a top surface of a bottom of the movable drawer.

35. The apparatus of claim 34, comprising a lift mechanism operatively connected to the vertically oriented storage unit and configured to move the vertically oriented storage unit between the positions above the deck and positions below the deck and within the movable drawer.

36. The apparatus of any one of claims 34-35, wherein the gripper assembly comprises a horizontally oriented gripping apparatus mounted on a cross-bay gantry positioned within the cabinet.

37. The apparatus of claim 36, wherein the apparatus comprises a pipettor and a vertically oriented gripping apparatus mounted on the cross-bay gantry.

38. The apparatus of claim 34, wherein the gripper assembly is mounted to the deck of the consumables bay.

39. The apparatus of any one of claims 34-38, wherein the vertically oriented storage unit comprises a plurality of horizonal shelves, each shelf of the plurality of horizontal shelves configured to receive a consumable carrier of the plurality of consumable carriers.

40. The apparatus of claim 39, wherein the vertically oriented storage unit comprises a plurality of movable doors, each door aligned with a shelf space above one of the plurality of horizontal shelves.

41. The apparatus of any one of claims 34-38, wherein the vertically oriented storage unit comprises a plurality of drawers, each of the drawers configured to receive a consumable carrier of the plurality of consumable carriers.

42. A method, comprising: receiving a plurality of consumable carriers in a vertically oriented storage unit configured to move between positions above a deck of a consumables bay and positions below the deck and within a movable drawer of the consumables bay, the consumables bay being positioned within a working chamber defined and enclosed by a cabinet;preparing a nucleic acid library for sequencing in an assay bay positioned with the working chamber of the cabinet; removing a consumable carrier of the plurality of consumable carriers from the storage unit using a gripper assembly located within the cabinet; and placing the consumable carrier removed from the storage unit onto a staging area on a top surface of a bottom of the movable drawer using the gripper assembly.

43. The method of claim 42, comprising removing the consumable carrier from the staging area and placing the consumable carrier into the storage unit.

44. The method of any one of claims 42-43, wherein the gripper assembly comprises a horizontally oriented gripping apparatus mounted on a cross-bay gantry positioned within the cabinet.

45. The method of claim 44, wherein a pipettor and a vertically oriented gripping apparatus are mounted on the cross-bay gantry.

46. The method of claim 42, wherein the gripper assembly is mounted to the deck of the consumables bay.

47. The method of any one of claims 42-46, comprising loading the plurality of consumable carriers onto a plurality of horizonal shelves of the vertically oriented storage unit.

48. The method of claim 47, comprising loading the plurality of consumable carriers onto the plurality of horizonal shelves via a plurality of movable doors in the vertically oriented storage unit.

49. The method of any one of claims 42-46, comprising loading the plurality of consumable carriers into a plurality of drawers of the vertically oriented storage unit.

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