|
| 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.
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| 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
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| |
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| 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)
|
| GSM4752163 |
8-week mouse kidney snATAC-seq sample 1 |
| GSM4752164 |
8-week mouse kidney snATAC-seq sample 2 |
| GSM4752165 |
P0 mouse kidney scRNA-seq sample 1 |
| GSM4752166 |
adult mouse kidney scRNA-seq sample 1 |
| GSM4752167 |
P0 mouse kidney bulk ATAC-seq sample 1 |
| GSM4752168 |
P0 mouse kidney bulk ATAC-seq sample 2 |
| GSM4752169 |
3-week mouse kidney bulk ATAC-seq sample 1 |
| GSM4752170 |
3-week mouse kidney bulk ATAC-seq sample 2 |
| GSM4752171 |
8-week mouse kidney bulk ATAC-seq sample 1 |
| GSM4752172 |
8-week mouse kidney bulk ATAC-seq sample 2 |
|
| Relations |
| BioProject |
PRJNA660027 |
| SRA |
SRP279230 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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