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Series GSE157079 Query DataSets for GSE157079
Status Public on Aug 29, 2020
Title Single cell resolution regulatory landscape of the mouse kidney highlights cellular differentiation programs and renal disease targets
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Determining the epigenetic program that generates unique cell types in the kidney is critical for understanding cell-type heterogeneity during tissue homeostasis and injury response. Here, we profiled open chromatin and gene expression in developing and adult mouse kidneys at single cell resolution. We show critical reliance of gene expression on distal regulatory elements (enhancers). We define key cell type-specific transcription factors and major gene-regulatory circuits for kidney cells. Dynamic chromatin and expression changes during nephron progenitor differentiation demonstrated that podocyte commitment occurs early and is associated with sustained Foxl1 expression. Renal tubule cells followed a more complex differentiation, where Hfn4a was associated with proximal and Tfap2b with distal fate. Mapping single nucleotide variants associated with human kidney disease identified critical cell types, developmental stages, genes, and regulatory mechanisms. We provide a global single cell resolution view of chromatin accessibility of kidney development. The dataset is available via interactive public websites.
Overall design 2 P0 mouse kidney snATAC-seq samples, 3 adult mouse kidney snATAC-seq samples, 1 P0 mouse kidney scRNA-seq sample, 1 adult mouse kidney scRNA-seq sample, 2 P0 mouse kidney bulk ATAC-seq samples, 2 3-week mouse kidney bulk ATAC-seq samples, and 2 8-week mouse kidney bulk ATAC-seq samples
Contributor(s) Miao Z, Balzer MS, Ma Z, Liu H, Wu J, Shrestha R, Aranyi T, Susztak K
Citation(s) 33859189, 34426578
Submission date Aug 28, 2020
Last update date Sep 29, 2021
Contact name Katalin Susztak
Organization name University of Pennsylvania
Street address 3400 Civic Center Boulevard, 12th floor
City Philadelphia
State/province Pennsylvania
ZIP/Postal code 19104
Country USA
Platforms (2)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (13)
GSM4752160 P0 mouse kidney snATAC-seq sample 1
GSM4752161 P0 mouse kidney snATAC-seq sample 2
GSM4752162 3-week mouse kidney snATAC-seq sample 1
BioProject PRJNA660027
SRA SRP279230

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
GSE157079_P01-50_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pval.signal.bigwig 694.0 Mb (ftp)(http) BIGWIG
GSE157079_P02-50_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pval.signal.bigwig 1.3 Gb (ftp)(http) BIGWIG
GSE157079_P0_adult_clusters.txt.gz 340.6 Kb (ftp)(http) TXT
GSE157079_P0_adult_counts.rds.gz 122.9 Mb (ftp)(http) RDS
GSE157079_P0_adult_pheno.txt.gz 297.3 Kb (ftp)(http) TXT
GSE157079_P0_adult_umap.txt.gz 992.8 Kb (ftp)(http) TXT
GSE157079_P21-1-50_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pval.signal.bigwig 662.2 Mb (ftp)(http) BIGWIG
GSE157079_P21-2-50_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pval.signal.bigwig 539.4 Mb (ftp)(http) BIGWIG
GSE157079_P56-1-50_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pval.signal.bigwig 669.2 Mb (ftp)(http) BIGWIG
GSE157079_P56-2-50_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pval.signal.bigwig 471.1 Mb (ftp)(http) BIGWIG
GSE157079_snATAC_UMAP_coordinates.csv.gz 527.4 Kb (ftp)(http) CSV
GSE157079_snATAC_cell_by_peak_matrix.txt.gz 448.0 Mb (ftp)(http) TXT
GSE157079_snATAC_metadata.csv.gz 216.1 Kb (ftp)(http) CSV
GSE157079_snATAC_peak_list.csv.gz 4.8 Mb (ftp)(http) CSV
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Processed data are available on Series record

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