Process method for combined analysis of single-cell scRNA-seq and scATAC-seq

Abstract

The invention discloses a process method for combined analysis of single-cell scRNA-seq and scATAC-seq. The process method comprises the steps of scRNA-seq analysis, scATAC-seq analysis, scRNA-seq andscATAC-seq combined analysis. According to the invention, the method is scientific and reasonable in structure, is safe and convenient to use, and the analysis process is simple, convenient and novel; the method comprises the following steps: firstly, making scRNA-seq data. According to the invention, the gene difference analysis and cell clustering analysis are carried out at first; then, chromatin accessibility analysis is performed on the scATAC-seq data; footprint analysis and cell clustering analysis of transcription factors are carried out, and finally, the data of the transcription factors and the cell clustering analysis are subjected to copuledNMF joint analysis. In addition, five files originally required to be input into the coupledNMF are simplified into three necessary files,and the operation process is simplified, so the coupledNMF can become a language program capable of being operated and operated to perform data analysis.

Description

technical field [0001] The invention relates to the technical field of single cells, in particular to a process method for joint analysis of single cell scRNA-seq and scATAC-seq. Background technique [0002] Biological samples of interest in clinical or experimental research are usually heterogeneous mixtures of different types of cells. Omics research plays an important role in the mining of key genes in cells and in-depth analysis of gene network regulation. Single-cell sequencing is a large-scale Parallel sequencing method, which is an excellent method to study tumor heterogeneity, immune cell population and embryonic development, provides us with the largest onco-omics sequencing platform, and plays an important role in explaining the alteration of genetic pathways involved in human cancer and early embryonic development ; [0003] Single-cell RNA-seq sequencing obtains the gene expression profile of cells at the mRNA level, and constructs a newly determined subtype cl...

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Problems solved by technology

[0003] Single-cell RNA-seq sequencing obtains the gene expression profile of cells at the mRNA level, and constructs a newly determined subtype classification, enabling the identification and characterization of previously unknown cell subtypes and their gene markers, which provides a basis for the study of pathological mechanisms and the diagnosis of diseases. To provide assistance in diagnosis and treatment, recent literature reports that using single-cell RNA-Seq technology to construct gene expression profiles of bone marrow mononuclear cells, comparing the chimerism of donors and recipients, and mapping immune cell genes in the immune process of transplantation surgery Expression profiling, and discovered new immune cell subsets, single-cell ATAC-seq sequencing analyzes chromatin accessibility at the chromatin level, and draws the regulatory network of transcription factors involved in transcriptional regulation, which can reveal the interaction between transcription factors and trans The relationship between elements, this kind of open chromatin site mining analysis based on high-throughput sequencing can reveal different regulatory factor sites at the genome level, break the analysis boundaries between the upstream and downstream of a single gene and between chromosomes, and analyze the differentiation of human hematopoietic system cells. Perform scATAC-seq analysis of chromatin accessibility in different types, construct chromatin accessibility state change tracks in hematopoietic cell differentiation and mine key transcriptional regulators, combined analysis of scRNA-seq and scATAC-seq provides single-cell genes Dynamic and chromatin accessibility state change tracks, comprehensively analyze the process of gene transcription regulation at the chromatin level and expressed gene level, although single-cell scRNA-seq and scATAC-seq have more studies, but can be used for scRNA-seq There are few methods for joint analysis with scATAC-seq, especially the analysis method for the corresponding relationship between differentially expressed mRNAs and corresponding transcriptional regulatory factor target sites and accessible regions of chromatin has not yet appeared

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