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Sample GSM7458184 Query DataSets for GSM7458184
Status Public on Mar 11, 2024
Title RNAseq_ESC_wstf_ko_A_1
Sample type SRA
 
Source name embryonic stem cells
Organism Mus musculus
Characteristics tissue: embryonic stem cells
cell line: 129S6/SvEvTac
cell type: embryonic stem cells
genotype: wstf knock-out
treatment: none
Extracted molecule polyA RNA
Extraction protocol RNA was extracted with Qiagen Rneasy Mini Kit following manufacture's instruction.. Potential contaminating genomic DNA was removed using Invitrogen DNA-free removal kit, following manufacture's instructions.
Sequencing libraries were prepared from 100ng of purified total RNA using TruSeq stranded mRNA Library Prep (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. RNA-seq reads were mapped to mm10 using QuasR in spliced alignment mode (splicedAlignment = TRUE) with the option (aligner="Rhisat2"), which internally uses hisat2 (Kim, Paggi, Park et al, Nature Biotech 2019)
Alignments overlapping the opposite strand of any exon of a known gene (gene annotation from the Bioconductor package TxDb.Mmusculus.UCSC.mm10.knownGene, version 3.10.0) were counted using the qCount function from the QuasR Bioconductor package (Gaidatzis et al, Bioinformatics, 2015) with default parameters.
Assembly: mm10
Supplementary files format and content: csv, count table
 
Submission date Jun 06, 2023
Last update date Mar 11, 2024
Contact name Dirk Schuebeler
Organization name Friedrich Miescher Institute for Biomedical Research
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
 
Platform ID GPL17021
Series (2)
GSE234248 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [RNA-seq]
GSE234295 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF
Relations
BioSample SAMN35642062
SRA SRX20601776

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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