|
| Status |
Public on Feb 01, 2021 |
| Title |
CTRL1 |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Pdss2wt/kd
tissue: kidney
age: five months
Sex: male
|
| Treatment protocol |
Animals were euthanized by rapid carbon dioxide narcosis followed by cervical dislocation after disease onset (5 months). Kidneys were quickly removed. One kidney was frozen in the liquid phase of isopentane, pre-cooled toward its freezing point (-80°C) with dry ice and the second kidney was fixed in neutral buffered formalin. Experiments were performed in 3 mice for each group.
|
| Growth protocol |
Mice were housed and bred according to the international standard conditions, with a 12-hour light/12-hour dark cycle and free access to food and water.
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Nuclei isolation as described in corresponding publication.
Single nuclei were processed through the 10X Chromium 3' Single Cell Platform using the Chromium Single Cell 3’ Library, Gel Bead and Chip Kits (10X Genomics, Pleasanton, CA), following the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Cellranger toolkit (v2.1.1) used to perform de-multiplexing using the “cellranger mkfastq” command, and the “cellranger count” command for alignment to the mouse pre-mRNA transcriptome, cell barcode partitioning, collapsing unique molecular identifier (UMI) to transcripts, and gene-level quantification.
Genome_build: mm10, pre-mRNA
Supplementary_files_format_and_content: genes.tsv: This file contains all annotated genes; barcodes.tsv: This file contains the filtered barcodes (barcodes that were filtered as cells) represented in the mtx file; matrix.mtx: UMI counts per gene and barcode combination
|
| |
|
| Submission date |
Jan 05, 2021 |
| Last update date |
Feb 02, 2021 |
| Contact name |
Eriene-Heidi Sidhom |
| E-mail(s) |
eriene-heidi_sidhom@hms.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Street address |
4 Blackfan Circle HIM 536
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE164273 |
Single nucleus RNA sequencing of kidney from five-month-old Pdss2 kd/kd mice compared to age-matched controls |
| GSE164274 |
Targeting a Braf/Mapk pathway rescues podocyte lipid peroxidation in CoQ deficiency kidney disease |
|
| Relations |
| BioSample |
SAMN17216862 |
| SRA |
SRX9784673 |
