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Sample GSM5005601 Query DataSets for GSM5005601
Status Public on Feb 01, 2021
Title CTRL2
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 SAMN17216861
SRA SRX9784674

Supplementary file Size Download File type/resource
GSM5005601_CTRL2_barcodes.tsv.gz 19.3 Kb (ftp)(http) TSV
GSM5005601_CTRL2_genes.tsv.gz 212.7 Kb (ftp)(http) TSV
GSM5005601_CTRL2_matrix.mtx.gz 14.9 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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