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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 20, 2024 |
| Title |
P0 mouse, scRNA-seq, rep M9 |
| Sample type |
SRA |
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| Source name |
Kidney tissue
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| Organism |
Mus musculus |
| Characteristics |
tissue: Kidney tissue
strain: C57BL6/J
cell type: Kidney cells
age: at day of birth (postnatal day 0)
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Harvested P0 mouse kidneys were dissected into smaller pieces in cold Dulbecco’s phosphate-buffered saline (DPBS Ca2+-/Mg2+-, Gibco 14190-250). For cell isolations, the Bacillus licheniformis cold active protease (CAP) protocol was used to dissociate kidney tissue into cells as previously described in (Ransick et al., 2019). Briefly, tissue was lysed in the DPBS lysis buffer, with the final concentration of a 2.5 mg/ml type 2 collagenase (Worthington, #LS00417), 7.5 mg/ml B. licheniformis protease (Creative Enzymes, NATE-0633), and 125 U/ml DNase I (Worthington, #LS002058) at 12°C. After 30 mins of digestion, the reaction was terminated with 20% fetal bovine serum (FBS) in DPBS. Cells were then strained through coarse 40 um cell strainers (Falcon, #352340) and pelleted at 364g in a swinging bucket centrifuge at 6oC. Cells were resuspended in cold AutoMACs Running Buffer (AMB, Miltenyi Biotec) and strained again with fine mesh 40um strainer (VWR, #76327-098). Live cells with DNA staining (DAPI-/DRAQ5+) were sorted by ARIA II FACS (BD Biosciences) and pelleted at 350g for 10mins then resuspended in ice cold AMB.
Chromium_SingleCell_3'_ReagentKits_v2/v3_UserGuide (CG00052, CG000183)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
10X Chromium Single Cell 3' v3
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| Data processing |
Sequencing reads were aligned to the mouse genome (mm10-3.0.0) with the Cell Ranger software (version 3.0.2) using STAR aligner on the University of Southern California High Performance Cluster. The samples were aggregated using cellranger aggr. The files from "filtered_feature_bc_matrix" folders are provided (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) compressed into tar.gz files.
Assembly: mm10-3.0.0
Supplementary files format and content: barcodes.tsv.gz
Supplementary files format and content: features.tsv.gz
Supplementary files format and content: matrix.mtx.gz
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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 |
GPL21103 |
| Series (2) |
| GSE232481 |
Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development [mouse scRNA-seq] |
| GSE232482 |
Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development |
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| Relations |
| BioSample |
SAMN35069134 |
| SRA |
SRX20326315 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7337041_mouse_scRNA-seq_P0_M9_filtered_feature_bc_matrix.tar.gz |
69.7 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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