Research and develop a toolkit for single-cell sequencing and analysis of TEs expression

The Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences (hereinafter referred to as the Guangzhou Institute of Health) Chen Jiekai's group and the Southern University of Science and Technology Andrew Hutchins's group have jointly developed the single-cell sequencing and analysis toolkit scTE for transposable element expression.

Transposable elements (TEs) are the most abundant genetic information in the human genome, and refer to a type of DNA sequence that can move within the genome.

According to reports, single-cell transcriptome sequencing (scRNA-seq) is an excellent technique for studying the state of cell fate.

To fill the gap in this research, researchers have developed a bioinformatics toolkit-scTE that can simultaneously quantify the expression of genes and TEs from scRNA-seq data.

In order to solve this problem, and because conventional scRNA-seq has only short sequencing read length, scTE adopts a quantitative strategy for the TEs family level.

Compared with scRNA-seq to study the transcriptome, single-cell ATAC-seq (scATAC-seq) and other single-cell genomics technology research objects are chromatin.

However, single-cell genome sequencing data represented by scATAC-seq has several characteristics: 1.

The researchers proposed that due to the characteristics of multiple copies of TEs, the sparseness of data can be removed by accumulating TEs signals, and the dimensionality of the data can be reduced, which may be able to effectively solve the above problems of scATAC-seq data.

Related paper information: org/10.