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Series GSE130399 Query DataSets for GSE130399
Status Public on Nov 01, 2019
Title An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome
Organisms Homo sapiens; Mus musculus
Experiment type Other
Summary Simultaneous profiling of transcriptome and chromatin accessibility within single cells is a powerful approach to dissect gene regulatory programs in complex tissues. However, the 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.

*** For cell-gene/bin-counts matrix of fetal forebrain and adult cerebral cortex, please download from:
Overall design Combined analysis of RNA and accessible chromatin in single-cells.
Contributor(s) Zhu C, Yu M, Ren B
Citation(s) 31695190
NIH grant(s)
Grant ID Grant title Affiliation Name
U54 HG006997 Center for Mammalian Regulatory Genomics Ludwig Institute for Cancer Research Ltd Bing Ren
Submission date Apr 26, 2019
Last update date Apr 27, 2020
Contact name Zhu Chenxu
Organization name New York Genome Center
Street address 101 Avenue of the Americas
City New York
State/province New York
ZIP/Postal code 10044
Country USA
Platforms (3)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
GPL22245 Illumina HiSeq 2500 (Homo sapiens; Mus musculus)
Samples (16)
GSM3737488 Cell Mix DNA
GSM3737489 Cell Mix RNA
GSM3737490 Adult Cerebral Cortex Lib#1 DNA
BioProject PRJNA539985
SRA SRP194005

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE130399_GSM3737488_GSM3737489_Cell_Mix.tar.gz 37.3 Mb (ftp)(http) TAR
GSE130399_GSM3737490-GSM3737495_Adult_Cerebrail_Cortex.tar.gz 121.9 Mb (ftp)(http) TAR
GSE130399_GSM3737496-GSM3737499_Fetal_Forebrain.tar.gz 171.0 Mb (ftp)(http) TAR
GSE130399_RAW.tar 3.5 Mb (http)(custom) TAR (of BEDPE)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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