Space transcriptome chip and space transcriptome device
By setting location recognition sites and a specially arranged array of micropits in a spatial transcriptome chip, the problem of incomplete mRNA capture was solved, achieving higher capture density and integrity, and ensuring the accuracy of information acquisition.
Patent Information
- Application Number
- CN202423292061.8
- Authority / Receiving Office
- CN · China
- Patent Type
- Utility models(China)
- Current Assignee / Owner
- Filing Date
- 2024-12-31
- Publication Date
- 2026-01-20
- Estimated Expiration
- 2034-12-31
AI Technical Summary
In existing technologies, the mRNA capture integrity and density of spatial transcriptome chips are low, resulting in incomplete information acquisition.
In a spatial transcriptome chip, a first position recognition point is set at the edge of the chip substrate to identify the position of the chip substrate, and a second position recognition point is set in the slice sample capture area to identify the position of the slice sample capture area. A micro-pit array is arranged in the slice sample capture area, and the capture efficiency is improved by staggered or specific shape arrangement.
It effectively improved the integrity and density of mRNA capture, ensuring the accuracy and completeness of information acquisition.
Smart Images
Figure CN223813503U_ABST
Abstract
Description
Technical Field
[0001] This utility model relates to the field of space transcriptomics technology, and in particular to a space transcriptomics chip and a space transcriptomics device. Background Technology
[0002] Spatial transcriptomics aims to analyze gene expression data of tissue cells at the spatial level. The spatial transcriptomics information obtained by combining microscopic imaging and sequencing technologies includes cell type information, spatial information of cells, and transcriptomics information of cells.
[0003] Because selective gene expression is prevalent in different tissues within an individual and in different cells within the same tissue, this selective expression characterizes the different functions of cells at different time stages and spatial locations within the tissue. Spatial transcriptomics technology utilizes a chip containing differentially encoded solid microspheres loaded according to a specific pattern, which are brought into close contact with tissue slice samples to capture the transcriptomic information released by permeabilized cells. The location information of the encoded microspheres is obtained through fluorescence decoding under a microscope. By reverse transcription and library construction of cellular mRNA, the transcriptomic information of the cells is finally obtained through sequencing analysis. This information is then matched with the obtained spatial location information of the microspheres to create a spatial transcriptomic atlas of the tissue.
[0004] like Figures 1 to 5 As shown, the spatial transcriptome chip includes multiple slice sample capture regions 02 disposed on the chip substrate 01, for example... Figure 1 Four regions are set up: section sample capture area 02A, section sample capture area 02B, section sample capture area 02C, and section sample capture area 02D. Each section sample capture area 02 has micropits 03 on which coded microspheres are loaded. Before use, the coding information of the coded microspheres on the section sample capture area needs to be decoded to determine the spatial coding of the coded microspheres at each location in the section sample capture area. When using the spatial transcriptome chip, the tissue section sample is attached to the spatial transcriptome chip, and bright-field photography is performed using a microscope. The gaps in the spatial transcriptome data can be used as a basis for stitching together the bright-field images.
[0005] like Figure 3 Region B in the image represents a portion of the rectangular unit constituting the slice sample capture region; its enlarged view is shown below. Figure 4 As shown, Figure 4 The arrangement of capture micro-pits 03 in the rectangular constituent unit of the slice sample capture area is shown. In one specific setting, the capture micro-pits are circular micro-pits with a diameter of L7, which is 2μm and a depth of 1-2μm. The spacing L8 between adjacent micro-pits in the same row is 2μm, and the slice sample capture area is formed as a rectangular area with a side length of L4.
[0006] likeFigure 3 As shown, the solid line B represents a portion of the complete slice sample capture area. Figure 3 The unit 02 of the sample capture area is shown, which consists of a rectangular micro-pit array with a side length of L4. The length L4 is 200 μm, which needs to be smaller than the imaging range of the microscope so that the gaps between the rectangular areas can be captured, which is convenient for stitching the images. The sample capture area is provided with a first gap 04 and a second gap 05 between the rectangular micro-pit arrays. L5 and L6 are the lengths of the gaps between the rectangular micro-pit arrays.
[0007] However, L5 and L6 are the spacing gap lengths between the rectangular micro-pit arrays, and the first spacing gap 04 and the second spacing gap 05 on the capture area of the slice sample result in missing microsphere capture pits in both the longitudinal and transverse positions, which in turn leads to a decrease in the integrity and density of mRNA capture.
[0008] Therefore, how to improve the integrity and density of mRNA capture is a technical problem that urgently needs to be solved by those skilled in the art. Utility Model Content
[0009] The purpose of this invention is to provide a spatial transcriptome chip and spatial transcriptome device that improves the integrity and density of mRNA capture.
[0010] The spatial transcriptome chip provided in this application includes:
[0011] Encoded microspheres;
[0012] A chip substrate has a slice sample capture area on its substrate surface. The slice sample capture area has micropits for accommodating the coded microspheres. The micropit array is arranged in the slice sample capture area. The edge of the chip substrate has a first position recognition bit for identifying the position of the chip substrate. The slice sample capture area has a second position recognition bit for identifying the position of the slice sample capture area.
[0013] Optionally, in the above-mentioned spatial transcriptome chip, multiple slice sample capture regions are provided on the same chip substrate, and the second position identification bit is set on each slice sample capture region differently.
[0014] Optionally, in the above-mentioned spatial transcriptome chip, all the slice sample capture regions are arranged sequentially along the first direction.
[0015] Optionally, in the above-mentioned spatial transcriptome chip, the spacing between the capture regions of two adjacent slice samples along the first direction is the same.
[0016] Optionally, in the spatial transcriptome chip, the micro-pit array is arranged in the slice sample capture area, and the second position identification mark is located at a center position of the chip substrate and occupies an area of one micro-pit.
[0017] Optionally, in the spatial transcriptome chip, the first position identification mark is a notch arranged at an edge corner position of the chip substrate.
[0018] Optionally, in the spatial transcriptome chip, the chip substrate is in a rectangular structure, and the first position identification mark is a cut plane connecting long and short edge positions of the chip substrate.
[0019] Optionally, in the spatial transcriptome chip, the second position identification mark is a non-central symmetric mark.
[0020] Optionally, in the spatial transcriptome chip, the second position identification mark is an English letter.
[0021] A spatial transcriptome device comprises a spatial transcriptome chip, which is any one of the spatial transcriptome chips described above.
[0022] In the technical solution, the spatial transcriptome chip comprises coded microspheres and a chip substrate, the substrate surface of the chip substrate is provided with a slice sample capture area, the slice sample capture area is provided with micro-pits for accommodating the coded microspheres, the micro-pit array is arranged in the slice sample capture area, the edge position of the chip substrate is provided with a first position identification mark for identifying the position of the chip substrate, and the slice sample capture area is provided with a second position identification mark for identifying the position of the slice sample capture area.
[0023] As can be seen from the above description, in the spatial transcriptome chip provided by the present application, the edge position of the chip substrate is provided with a first position identification mark for identifying the position of the chip substrate, and the slice sample capture area is provided with a second position identification mark for identifying the position of the slice sample capture area, so that the micro-pit array is arranged in the slice sample capture area, and the longitudinal and transverse positions of the slice sample capture area are effectively improved in the case of missing, thereby effectively improving the capture integrity and density of mRNA. BRIEF DESCRIPTION OF DRAWINGS
[0024] In order to more clearly illustrate the technical solutions in the embodiments of the present application or the prior art, the drawings needed in the following embodiment or prior art description will be briefly introduced. Obviously, the drawings in the following description are only embodiments of the present application, and other drawings can be obtained by those skilled in the art without creative labor on the basis of the provided drawings.
[0025] Figure 1It is a structural schematic view of a traditional spatial transcriptome chip;
[0026] Figure 2 It is a structural schematic view of a traditional slice sample capture area;
[0027] Figure 3 It is a structural schematic view of a traditional slice sample capture area; Figure 2 It is an enlarged view of A part of the slice sample capture area shown in the figure;
[0028] Figure 4 It is an enlarged view of B part of the slice sample capture area shown in the figure; Figure 3
[0029] It is a partial enlarged view of the slice sample capture area; Figure 5
[0030] It is a structural schematic view of a first spatial transcriptome chip provided by an embodiment of the utility model; Figure 6
[0031] It is a partial enlarged view of the slice sample capture area provided by an embodiment of the utility model; Figure 7
[0032] It is a structural schematic view of a second spatial transcriptome chip provided by an embodiment of the utility model; Figure 8
[0033] It is a structural schematic view of a third spatial transcriptome chip provided by an embodiment of the utility model. Figure 9 Among them
[0034] In the middle: Figures 1-9
[0035] 01-chip base, 02-slice sample capture area, slice sample capture area 02A, slice sample capture area 02B, slice sample capture area 02C, slice sample capture area 02D, 03-micro pit, 04-first interval space, 05-second interval space;
[0036] 1-chip base, 2-slice sample capture area, 3-micro pit, 4-second position identification bit, 5-first position identification bit. DETAILED DESCRIPTION
[0037] The core of the utility model is to provide a kind of spatial transcriptome chip and spatial transcriptome equipment, and the capture integrity and density of mRNA are improved.
[0038] In order to make those skilled in the art better understand the technical scheme of the utility model, the utility model is further described in detail below in conjunction with the drawings and implementation.
[0039] Please refer to Figures 6 to 9 .
[0040] In a specific embodiment, the spatial transcriptome chip provided by the specific embodiment of the utility model includes coded microspheres and a chip substrate 1, the substrate surface of the chip substrate 1 is provided with a slice sample capture area 2, the slice sample capture area 2 is provided with micro pits 3 accommodating coded microspheres, the micro pits 3 are arrayed in the slice sample capture area 2, and the edge position of the chip substrate 1 is provided with a first position identification bit 5 identifying the position of the chip substrate 1.Specifically, the micro pits 3 are arrayed in the slice sample capture area 2 in a staggered manner, for example, the micro pits 02 in the same row and the micro pits 02 in the adjacent row close to each other are arranged in an equilateral triangle.
[0041] Specifically, the first position identification bit 5 can be a groove provided at the edge position of the chip substrate 1, or the first position identification bit 5 is a notch provided at the corner position of the chip substrate 1, or the first position identification bit 5 is an identification piece provided at the edge of the chip substrate 1 and protruding outward. By providing the first position identification bit 5, the approximate position of the spatial transcriptome chip can be identified.
[0042] In a specific embodiment, the chip substrate 1 can be circular. Preferably, the chip substrate 1 is of a rectangular structure, and the first position identification bit 5 is a tangent plane connecting the long side and the short side positions of the edge of the chip substrate 1.
[0043] The slice sample capture area 2 is provided with a second position identification bit 4 identifying the position of the slice sample capture area 2, and the second position identification bit 4 can be circular. The second position identification bit 4 serves as the basis for photo splicing. In order to accurately identify the accurate position of the slice sample capture area 2, preferably, the second position identification bit 4 is a non-central symmetric mark, for example, the second position identification bit 4 is a triangle or a square. In order to facilitate the identification of each second position identification bit 4, preferably, the second position identification bit 4 is an English letter, and according to the identification order of each slice sample capture area 2, the second position identification bits 4 on the slice sample capture area 2 are arranged in English order.
[0044] As can be seen from the above description, in the spatial transcriptome chip provided by the specific embodiment of the present application, the edge position of the chip substrate 1 is provided with a first position identification bit 5 identifying the position of the chip substrate 1, and the slice sample capture area 2 is provided with a second position identification bit 4 identifying the position of the slice sample capture area 2. The micro pits 3 are arrayed in the slice sample capture area 2, that is, the present application completes the capture of the cell mRNA in the slice tissue sample, and the size and density of the micro pits 3 determine the capture resolution of the chip. Specifically, the notch of the chip substrate 1 is used as a positioning corner, and the second position identification bit 4 is used as a positioning mark to complete the splicing of the photos, without the need to set the missing micro pits 3, thereby improving the capture integrity and density of the mRNA.
[0045] In an embodiment, the chip substrate 1 is provided with a plurality of slice sample capture areas 2, and the second position identification bit 4 provided on each slice sample capture area 2 is different.
[0046] In an embodiment, all the slice sample capture areas 2 are arranged in sequence along the first direction. For example, all the slice sample capture areas 2 are arranged in sequence along the horizontal direction. The interval between adjacent slice sample capture areas 2 can be different.
[0047] In an embodiment, the interval between two adjacent slice sample capture areas 2 along the first direction is the same, so as to facilitate the positioning of the slice sample capture areas 2.
[0048] In an embodiment, the second position identification bit 4 is located at the center of the chip substrate 1, and the second position identification bit 4 is used for positioning and calibration of each photographing area position.
[0049] In order to facilitate understanding, the following will be described in combination with a specific use method. The first position identification bit 5 is used to complete the positioning of the spatial transcriptome chip and the automatic displacement platform of the microscope. After positioning, the complete spatial transcriptome chip coordinates can be recognized by the automatic displacement platform of the microscope, so as to find the second position identification bit 4 and complete the maximum mRNA information capture of the slice sample.
[0050] The spatial transcriptome device provided in the present application comprises the spatial transcriptome chip, and the spatial transcriptome chip is any one of the above-described spatial transcriptome chips. The foregoing describes the specific structure of the spatial transcriptome chip, and the present application comprises the above-described spatial transcriptome chip and also has the above-described technical effects.
[0051] The embodiments in the specification are described in a progressive manner, and each embodiment focuses on the difference from other embodiments. The same or similar parts between the embodiments can be referred to each other.
[0052] The above description of the disclosed embodiments enables a person skilled in the art to implement or use the present application. Various modifications to these embodiments will be apparent to those skilled in the art, and the general principles defined herein can be implemented in other embodiments without departing from the spirit or scope of the present application. Therefore, the present application will not be limited to the embodiments shown herein, but will conform to the widest scope consistent with the principles and novel features disclosed herein.
Claims
1. A spatial transcriptome chip, characterized in that, include: Encoded microspheres; A chip substrate (1) has a slice sample capture area (2) on its base surface. The slice sample capture area (2) has micro-pits (3) for accommodating the coded microspheres. The micro-pits (3) are arranged in an array in the slice sample capture area (2). The edge of the chip substrate (1) has a first position recognition bit (5) for identifying the position of the chip substrate (1). The slice sample capture area (2) has a second position recognition bit (4) for identifying the position of the slice sample capture area (2).
2. The spatial transcriptome chip according to claim 1, characterized in that, Multiple slice sample capture areas (2) are provided on the same chip substrate (1), and the second position identification bit (4) is different on each slice sample capture area (2).
3. The spatial transcriptome chip according to claim 2, characterized in that, All the sliced sample capture regions (2) are arranged sequentially along the first direction.
4. The spatial transcriptome chip according to claim 2, characterized in that, The two adjacent slice sample capture regions (2) are spaced at the same distance along the first direction.
5. The spatial transcriptome chip according to claim 1, characterized in that, The micro-pits (3) array is arranged in the slice sample capture area (2), and the second position identification position (4) is located at the center of the chip substrate (1) and occupies the area of one of the micro-pits (3).
6. The spatial transcriptome chip according to claim 1, characterized in that, The first position identification bit (5) is a notch located at the corner of the edge of the chip substrate (1).
7. The spatial transcriptome chip according to claim 6, characterized in that, The chip substrate (1) has a rectangular structure, and the first position identification position (5) is a tangent plane connecting the long side and the short side of the edge of the chip substrate (1).
8. The spatial transcriptome chip according to any one of claims 1-7, characterized in that, The second position identification bit (4) is a non-central symmetric identifier.
9. The spatial transcriptome chip according to claim 8, characterized in that, The second position identification bit (4) is an English letter.
10. A space transcriptome device, characterized in that, Includes a spatial transcriptome chip, wherein the spatial transcriptome chip is the spatial transcriptome chip according to any one of claims 1-9.