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Series GSE216371 Query DataSets for GSE216371
Status Public on Apr 14, 2024
Title A single-cell atlas of chromatin accessibility in mouse organogenesis
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Recent surveys of mouse organogenesis cell atlas (MOCA) with single cell transcriptomics have uncovered hundreds of cell types, but the cell-type-specific transcriptional regulatory programs responsible for the unique identity and function of each cell type have yet to be elucidated. We applied a four-level combinatorial indexing assay, SPATAC-seq, to profile the chromatin accessibility in >350,000 cells derived from 13 embryos staged between embryonic day (E) 10.5 and 13.5 in a single experiment. The resulting map revealed the status of open chromatin for 844,817 candidate cis-regulatory elements (cCREs) in 33 main cell types and 296 subtypes. By integrating this accessible chromatin atlas with scRNA data of MOCA, we characterized the gene regulatory sequences and transcription factors associated with cell fate commitment, such as unreported role of Nr5a2 and Gata6 in gastrointestinal tract. Finaly, we integrated this atlas with previous scATAC-seq data from mouse embryos at E8.25 and 13 adult mouse tissues to dissect life stage specific gene regulatory programs across different cell types. This rich resource and comprerhensive analysis provide a foundation for expolring gene regulators in mammalian cell differentiation.
 
Overall design Nuclei from different mice embryos at embryonic day (E) 10.5, E11.5, E12.5 and E13.5 were extracted by previously described methods (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Then extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment.
 
Contributor(s) Sun K, Lan X
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Submission date Oct 23, 2022
Last update date Apr 15, 2024
Contact name Keyong Sun
E-mail(s) keyongsuntsinghua@gmail.com
Organization name tsinghua university
Department School of Medicine
Street address Hai Dian street
City beijing
ZIP/Postal code 100084
Country China
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (68)
GSM6671097 SPATAC-seq with mouse organogenesis well-E11A
GSM6671098 SPATAC-seq with mouse organogenesis well-E11B
GSM6671099 SPATAC-seq with mouse organogenesis well-E11C
Relations
BioProject PRJNA893359

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

Supplementary file Size Download File type/resource
GSE216371_Cell_annotation_and_cCREs_in_MOPA.xlsx 114.5 Mb (ftp)(http) XLSX
GSE216371_MOPA_bigWig_file.tar.gz 10.2 Gb (ftp)(http) TAR
GSE216371_RAW.tar 70.9 Gb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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