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Sample GSM5133961 Query DataSets for GSM5133961
Status Public on Nov 30, 2021
Title CPC_Bl6N_1
Sample type SRA
 
Source name Cardiac Side Population from wild-type mouse
Organism Mus musculus
Characteristics sorting date: 2016-08-22
strain: C57BL/6NRj
Extracted molecule polyA RNA
Extraction protocol RNA was isolated from a total of three sorts of SP-CPCs using the NucleoSpin RNA XS kit (Macherey Nagel).
Each sort consisted of the cardiomyocyte- and erythrocyte-depleted cardiac cell suspension from 4 wt and 4 flt3L-/- mice.
RNA quality was controlled on an Agilent 2100 Bioanalyzer using RNA Pico CHIP (Agilent Technologies).
RNA-seq library preparation and sequencing were performed at the Quantitative Genomics Facility of the D-BSSE of the ETHZ (Basel, Switzerland).
RNA-seq library quality was assessed with a Fragment Analyzer (Advanced Analytical).
Unstranded RNA-seq libraries were produced using the low-input SMART-Seq v4 kit (Clontech/Takara).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description gene_counts.tsv.gz
Data processing Reads were aligned to the mouse genome (mm10) using the spliced read aligner STAR (version 2.5.2a_modified) with default parameters, except reporting only one hit in the final alignment for multimappers (outSAMmultNmax=1) and filtering reads without evidence in the spliced junction table (outFilterType=“BySJout”).
Sequencing and mapping quality was assessed by the qQCReport function of the R package QuasR (version 1.18) and with FastQC (version 0.11.3).
Gene expression was quantified by the qCount function of the R Bioconductor package QuasR (version 1.18) as the number of reads that started within any annotated exon of a gene from the Ensembl 88 annotation (irrespective of strand).
Genome_build: mm10
Supplementary_files_format_and_content: gzipped text file with tab-separated counts for each gene; each row contains the annotation and raw counts per gene; columns correspond to: 1. Ensembl Gene ID (release 88), 2.-7. read counts per gene and sample.
 
Submission date Mar 03, 2021
Last update date Nov 30, 2021
Contact name DBM Bioinformatics Core Facility
Phone +41612073541
Organization name University of Basel
Department Departement of Biomedicine
Street address Hebelstrasse 20
City Basel
State/province BS
ZIP/Postal code 4053
Country Switzerland
 
Platform ID GPL19057
Series (1)
GSE168207 Fms-like tyrosine kinase 3 (Flt3) contributes to a receptor tyrosine kinase signature regulating the cardiac side population
Relations
BioSample SAMN18133114
SRA SRX10234860

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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