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Series GSE140203 Query DataSets for GSE140203
Status Public on Oct 23, 2020
Title Integrative single-cell chromatin and transcriptome profiling uncovers cell-type specific regulatory interactions
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Simultaneous measurement of different molecular aspects of gene regulation can help infer functional relationships between genome regulation and gene expression, and understand their distinct and contribution to cell phenotype. Here, we present SHARE-seq, a highly scalable, sensitive, and cost-effective approach for joint measurement of chromatin accessibility and gene expression from the same single cells. Applying SHARE-seq to adult mouse tissues (skin, brain, lung) we show a direct congruence in cell type definition by either chromatin accessibility or RNA expression and create cell-type specific regulatory maps. We leverage naturally occurring cell-cell variation to infer chromatin-expression regulatory relationships and develop a broadly applicable computational strategy to define cis- ad trans- regulatory programs. The cis-regulatory programs, which largely overlap with super-enhancers, are found at key lineage-specifying genes. We demonstrate dynamic chromatin evidence of both gene expression lineage-priming and lineage-memory. The combined scalability and depth of SHARE-seq provide an extensible platform to study the regulatory relationships governing chromatin and gene expression changes across diverse cells within tissues.
Overall design SHARE-seq to profile chromatin accessibility and gene expression in the same cell from cell lines (GM12878, 3T3, K562, Raw 267.4), mouse skin, brain, and lung.
Contributor(s) Ma S, Buenrostro J
Citation(s) 33098772
Submission date Nov 11, 2019
Last update date Oct 04, 2022
Contact name Sai Ma
Organization name Icahn School of Medicine at Mount Sinai
Street address 1425 Madison Ave
City New York
ZIP/Postal code 10026
Country USA
Platforms (4)
GPL21626 NextSeq 550 (Mus musculus)
GPL21697 NextSeq 550 (Homo sapiens)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (20)
GSM4156590 GM12878 rep1 (ATAC-Seq)
GSM4156591 GM12878 rep2 (ATAC-Seq)
GSM4156592 GM12878 rep3 (ATAC-Seq)
BioProject PRJNA588784
SRA SRP229493

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Supplementary file Size Download File type/resource
GSE140203_RAW.tar 7.4 Gb (http)(custom) TAR (of BED, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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