|
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).
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|
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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.
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|
|
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 |