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Series GSE153479 Query DataSets for GSE153479
Status Public on Dec 08, 2020
Title Single cell ATAC-seq of neonatal heart regeneration
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The adult mammalian heart has limited capacity for regeneration following injury, whereas the neonatal heart can readily regenerate within a short period after birth. Neonatal heart regeneration is orchestrated by multiple cell types intrinsic to the heart, as well as immune cells that infiltrate the heart after injury. To elucidate the transcriptional responses of the different cellular components of the mouse heart following injury, we performed single cell RNA-sequencing on neonatal hearts at various time points following myocardial infarction, and coupled the results with bulk tissue RNA-sequencing data collected at the same time points. Concomitant single cell ATAC-sequencing exposed underlying dynamics of open chromatin landscapes and regenerative gene regulatory networks of diverse cardiac cell types, and revealed previously unknown mediators of cardiomyocyte proliferation, angiogenesis and fibroblast activation. Together, our data provide a transcriptional basis for neonatal heart regeneration at single cell resolution and suggest new strategies for enhancing cardiac function in response to injury.
 
Overall design We performed myocardial infarction (MI) or sham surgeries to mouse hearts at postnatal day 1 or day 8. At 3d post P1 and P8 surgery, ventricle samples below the surgery plane were collected for single cell ATAC-Seq.
 
Contributor(s) Wang Z, Tan W, Olson E
Citation(s) 33296652
Submission date Jun 29, 2020
Last update date Jan 04, 2021
Contact name Zhaoning Wang
E-mail(s) zhw063@health.ucsd.edu
Organization name UC San Diego
Department Cellular and Molecular Medicine
Lab Bing Ren Lab
Street address 9500 Gilman Drive
City La Jolla
State/province California
ZIP/Postal code 92093
Country USA
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (4)
GSM4644945 scATAC-seq_P1_3MI
GSM4644946 scATAC-seq_P1_3Sham
GSM4644947 scATAC-seq_P8_3MI
This SubSeries is part of SuperSeries:
GSE153481 Cell-type-specific gene regulatory networks underlying murine neonatal heart regeneration at single-cell resolution
Relations
BioProject PRJNA642813
SRA SRP269201

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
GSE153479_description.txt.gz 151 b (ftp)(http) TXT
GSE153479_filtered_peak_bc_matrix.h5 289.6 Mb (ftp)(http) H5
GSE153479_filtered_peak_bc_matrix_barcodes.tsv.gz 166.8 Kb (ftp)(http) TSV
GSE153479_filtered_peak_bc_matrix_matrix.mtx.gz 594.0 Mb (ftp)(http) MTX
GSE153479_filtered_peak_bc_matrix_peaks.bed.gz 944.4 Kb (ftp)(http) BED
GSE153479_fragments.tsv.gz 8.0 Gb (ftp)(http) TSV
GSE153479_fragments.tsv.gz.tbi.gz 2.0 Mb (ftp)(http) TBI
GSE153479_singlecell.csv.gz 16.0 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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