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| Status |
Public on Jun 21, 2024 |
| Title |
Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development [human ATAC-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Mammalian kidneys maintain fluid homeostasis through the cellular activity of nephrons and the conjoined collecting system. Each epithelial network originates from distinct progenitor cell populations that reciprocally interact during development. To extend our understanding of human and mouse kidney development, we profiled chromatin organization (ATAC-seq) and gene expression (RNA-seq) in developing human and mouse kidneys. Data were analyzed at a species level and then integrated into a common, cross-species multimodal data set. Comparative analysis of cell types and developmental trajectories identified conserved and divergent features of chromatin organization and linked gene activity, revealing species- and cell-type specific regulatory programs. Identification of human-specific enhancer regions linked through GWAS studies to kidney disease highlights the potential of developmental modeling to provide clinical insight.
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| Overall design |
Human donor fetal kidneys were obtained, dated and dissected by the Obstetrics and Gynecology Maternal Fetal Medicine Division of University of Southern California. Fetal embryonic age is estimated based on first day of last menstrual period (LMP). Non-nucleotide, processed feature-barcode information is provided.
***Controlled access to raw fastq files is available through dbGaP***
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| Contributor(s) |
Kim S, Koppitch K, Parvez RK, Guo J, Achieng M, Schnell J, Lindström NO, McMahon AP |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
May 13, 2023 |
| Last update date |
Jun 22, 2024 |
| Contact name |
Andrew P McMahon |
| E-mail(s) |
amcmahon@med.usc.edu
|
| Phone |
323-442-7847
|
| Organization name |
University of Southern California
|
| Department |
Stem Cell Biol & Regen Med
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| Lab |
Andrew McMahon
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| Street address |
1425 San Pablo St, BCC 312
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| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90033 |
| Country |
USA |
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| Platforms (2) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
| GPL28038 |
DNBSEQ-G400 (Homo sapiens) |
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| Samples (9)
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| GSM7337007 |
10.6 Wk human fetal, snATAC-seq, rep M1 |
| GSM7337008 |
11.1 Wk human fetal, snATAC-seq, rep M2 |
| GSM7337009 |
11.6 Wk human fetal, snATAC-seq, rep M3 |
| GSM7337010 |
11.3 Wk human fetal, snATAC-seq, rep F1 |
| GSM7337011 |
11.2 Wk human fetal, snATAC-seq, rep F2 |
| GSM7337012 |
17.1 Wk human fetal, snATAC-seq, rep M4 |
| GSM7337013 |
17.5 Wk human fetal, snATAC-seq, rep M5 |
| GSM7337014 |
17.1 Wk human fetal, snATAC-seq, rep F3 |
| GSM7337015 |
17.6 Wk human fetal, snATAC-seq, rep F4 |
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| This SubSeries is part of SuperSeries: |
| GSE232482 |
Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development |
|
| Relations |
| BioProject |
PRJNA972293 |
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