Open AccessAn ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome
Author(s) -
Chenxu Zhu,
Miao Yu,
Hui Huang,
Ivan Jurić,
Armen Abnousi,
Rong Hu,
Jacinta Lucero,
M. Margarita Behrens,
Ming Hu,
Bing Ren
Publication year - 2019
Publication title -
nature structural and molecular biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.448
H-Index - 270
eISSN - 1545-9993
pISSN - 1545-9985
DOI - 10.1038/s41594-019-0323-x
Subject(s) - chromatin , transcriptome , forebrain , biology , enhancer , computational biology , chia pet , gene , microbiology and biotechnology , genetics , transcription factor , gene expression , neuroscience , chromatin remodeling , central nervous system
Simultaneous profiling of transcriptome and chromatin accessibility within single cells is a powerful approach to dissect gene regulatory programs in complex tissues. However, current tools are limited by modest throughput. We now describe an ultra high-throughput method, Paired-seq, for parallel analysis of transcriptome and accessible chromatin in millions of single cells. We demonstrate the utility of Paired-seq for analyzing the dynamic and cell-type-specific gene regulatory programs in complex tissues by applying it to mouse adult cerebral cortex and fetal forebrain. The joint profiles of a large number of single cells allowed us to deconvolute the transcriptome and open chromatin landscapes in the major cell types within these brain tissues, infer putative target genes of candidate enhancers, and reconstruct the trajectory of cellular lineages within the developing forebrain.