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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 20, 2024 |
| Title |
11.1 Wk human fetal, snATAC-seq, rep M2 |
| Sample type |
SRA |
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| Source name |
Kidney tissue
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Kidney tissue
cell type: Kidney cells
age: 11.1 Wk human fetal
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
From the harvested P0 mouse kidneys, nuclei were isolated as previously described in(Wilson et al., 2019). Briefly, flash frozen kidney pieces were thawed on ice and dissected into smaller pieces (<1mm) with a razor blade and then dounced in cold Nuclei EZ Lysis Buffer (Sigma, N3408) supplemented with protease inhibitor (Roche; 05892791001) and RNAse inhibitors (Promega, N2615; Thermo Fisher Scientific, AM2696). The tissue was dounce grinded 30 times with a loose pestle (Sigma, P0485), and then filtered through a 200um strainer (pluriSelect, 43-50200). The tissue was dounce grinded 10 times with a tight pestle, and then incubated for 5 mins on ice. Cells were filtered through 40uM filter (pluriSelect ,43-50040) and pelleted at 500g for 5min at 4°C in a swinging bucket centrifuge. Supernatant was removed and nuclei pellet resuspended in Nuclei EZ lysis buffer with RNAse inhibitors, incubated an additional 5 mins on ice and pelleted again. The final pellet was resuspended in 4°C Nuclei Buffer (10X Genomics, #2000207).
Chromium_NextGEM_SingleCell_ATAC_ReagentKits_v1.1_UserGuide (CG000209)
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
DNBSEQ-G400 |
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| Description |
10X Chromium Single Cell ATAC v1.1
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| Data processing |
Sequencing reads were aligned to the mouse genome (atac-GRCh38-1.2.0) with the Cell Ranger atac software (version 1.2.0) using STAR aligner on the University of Southern California High Performance Cluster. The samples were aggregated using cellranger-atac aggr. Non-nucleotide, processed feature-barcode information is provided. Controlled access to raw fastq files is available through dbGaP. The files used in the analysis are provided (fragments.tsv.gz, fragments.tsv.gz.tbi, singlecell.csv, filtered_peak_bc_matrix.h5) compressed into tar.gz files.
Assembly: atac-GRCh38-1.2.0
Supplementary files format and content: fragments.tsv.gz
Supplementary files format and content: fragments.tsv.gz.tbi
Supplementary files format and content: singlecell.csv
Supplementary files format and content: filtered_peak_bc_matrix.h5
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| Submission date |
May 13, 2023 |
| Last update date |
Jun 20, 2024 |
| Contact name |
Andrew P McMahon |
| E-mail(s) |
amcmahon@med.usc.edu
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| Phone |
323-442-7847
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| Organization name |
University of Southern California
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| 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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| Platform ID |
GPL28038 |
| Series (2) |
| GSE232478 |
Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development [human ATAC-seq] |
| GSE232482 |
Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM7337008_Human_snATAC-seq_11.1Wk_M2_filtered_peak_bc_matrix_fragments_singlecell.tar.gz |
2.8 Gb |
(ftp)(http) |
TAR |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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