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| Status |
Public on Nov 01, 2024 |
| Title |
Whole kidney P2 control |
| Sample type |
SRA |
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| Source name |
control
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| Organism |
Mus musculus |
| Characteristics |
tissue: whole kidney
developmental stage: P2
strain: C57BL/6J
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
We harvested 1 kidney from C57BL/6J control and DM_Exp mice at P2 and generated single cell suspensions using 0.05% trypsin at 37°C for 10 minutes. Kidneys were mechanically dissociated with pipetting at 5 and 10 min. 3% fetal calf serum (FCS) in PBS was added to halt the trypsin. The cell suspension was filtered using a 40 μm filter and pelleted. The cells were resuspended in 90% FCS in DMSO and frozen.
Single-cell library preparation and sequencing was performed by GENEWIZ Inc. using the 10X Genomics Inc. Chromium 3’ Single Cell v2 library preparation kit
scRNA-seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Cellranger v 2.2.0 (10X Genomics)
Cell filtering, QC and normalization (DropletUtils, scds, scater, scran)
Genome_build: mm10
Supplementary_files_format_and_content: mtx, csv, txt; genes, barcodes, metadata, counts, log-counts
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| Submission date |
Nov 28, 2020 |
| Last update date |
Nov 01, 2024 |
| Contact name |
Dennis Kostka |
| E-mail(s) |
kostka@pitt.edu
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| Organization name |
University of Pittsburgh
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| Department |
Developmental Biology
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| Street address |
530 45TH ST
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| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15201 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE162298 |
Identifying the molecular mechanisms that underlie impaired kidney development due to maternal diabetes. |
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| Relations |
| BioSample |
SAMN16949072 |
| SRA |
SRX9600343 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4948612_GEO_736_barcodes.txt.gz |
36.7 Kb |
(ftp)(http) |
TXT |
| GSM4948612_GEO_736_counts.mtx.gz |
38.4 Mb |
(ftp)(http) |
MTX |
| GSM4948612_GEO_736_genes.txt.gz |
32.6 Kb |
(ftp)(http) |
TXT |
| GSM4948612_GEO_736_log-norm-counts.mtx.gz |
47.4 Mb |
(ftp)(http) |
MTX |
| GSM4948612_GEO_736_metadata.csv.gz |
777.8 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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