Unlock instant, AI-driven research and patent intelligence for your innovation.

Hi-C high-throughput sequencing and library building method suitable for plants

A high-throughput, sequencing technology, applied in the field of Hi-C high-throughput sequencing library construction, can solve problems such as impact, insufficient cross-linking and fixation, and affect the quality of Hi-C libraries, so as to improve data quality and improve availability Effect of data rate

Inactive Publication Date: 2020-04-28
INST OF COTTON RES CHINESE ACAD OF AGRI SCI
View PDF0 Cites 5 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Compared with animal cells, plant cells have insufficient cross-linking and fixation due to cell walls and vacuoles, and secondary metabolites affect the enzymatic reactions in the Hi-C process, thereby affecting the quality of the Hi-C library
This situation has always been the bottleneck for the establishment of high-quality Hi-C libraries in plant cells

Method used

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • Hi-C high-throughput sequencing and library building method suitable for plants
  • Hi-C high-throughput sequencing and library building method suitable for plants
  • Hi-C high-throughput sequencing and library building method suitable for plants

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0056] Example 1, Hi-C high-throughput sequencing of cotton

[0057] In this embodiment, the callus in the cotton tissue culture process is taken as the research object.

[0058] 1. Sample pretreatment

[0059] The method of the invention :

[0060] 1. Blot the fresh cotton callus with filter paper, and take 1 g of it, quick-freeze it in liquid nitrogen and grind it into powder.

[0061] 2. Transfer the ground cotton callus powder to the pre-frozen cross-linking solution at -90°C, and then slowly increase the temperature in gradients, -90°C—60°C—-30°C, and each temperature gradient lasts for 6 hours. Replace the water in the cells with the alcohol solution.

[0062] 3. Centrifuge at 5000rpm at 4°C for 30s to remove the alcohol solution, and then wash with NIBuffer buffer placed on ice for three times. After washing, add 20 mL of pre-cooled ( NIBuffer (pre-cooled on ice) to form a suspension and shake gently for 15 min.

[0063] 4. The suspension was filtered twice with ...

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

PUM

No PUM Login to View More

Abstract

The invention discloses a Hi-C high-throughput sequencing and library building method suitable for plants. The invention provides a sample pretreatment method suitable for Hi-C high-throughput sequencing and library establishment. The method comprises the following steps: freezing a biological sample to be tested, and then performing cross-linking and fixing. According to the invention, quality ofa library obtained by a process that a sample is subjected to crosslinking after being treated by using liquid nitrogen is evaluated, and it is found that in the cotton, almost no obvious three-dimensional conformational change exists between a fresh sample and a liquid nitrogen frozen sample; and moreover, data quality of a cotton Hi-C library can be greatly improved by carrying out pretreatmenton the sample by using a mode of ''performing freezing first and then performing crosslinking''. The invention breaks through limitation of Hi-C samples and provides a wider prospect for applicationof Hi-C in plant research.

Description

technical field [0001] The invention relates to the technical field of gene sequencing, in particular to a Hi-C high-throughput sequencing library construction method suitable for plants. Background technique [0002] Chromosome is a special structure that exists in the nucleus. According to the principle of "structure determines function", the three-dimensional (3D) structure of chromosome naturally becomes the basis for understanding its biological function. DNA genetic information is mainly composed of primary structure (nucleotide sequence) decision, but the 3D structure also played a crucial role. However, due to technical reasons, the progress in analyzing the 3D structure of chromosomes has been relatively slow. [0003] In 2002, Dekker et al established the 3C chromosome conformation capture (chromosome conformation capture, 3C) technology, which is a chromosome conformation technology for studying the interaction between chromosomes and proteins, and can analyze th...

Claims

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

Application Information

Patent Timeline
no application Login to View More
Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6806C40B50/06C12Q1/6869
CPCC12Q1/6806C40B50/06C12Q1/6869C12Q2523/101C12Q2535/122
Inventor 李付广郑武葛晓阳王晔陈艳丽
Owner INST OF COTTON RES CHINESE ACAD OF AGRI SCI