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Sample GSM4957589 Query DataSets for GSM4957589
Status Public on Sep 30, 2021
Title CD23-iCre rep2 - restingB (0hrs)
Sample type SRA
 
Source name spleen
Organism Mus musculus
Characteristics genotype: CD23-iCre
age: 8 weeks
cell type: B cells
condition: Resting
timepoint: 0hrs
Extracted molecule polyA RNA
Extraction protocol B cells (30x10e6) were lysed in 1ml of Trizol and 30μl of 1:100 diluted ERCC RNA Spike-In Mix (Ambion) was added to each lysate. RNA was isolated and eluted in a final volume of 20μl. 1μl of each sample was used for quality and concentration analysis on a 2100 Bioanalyzer using the RNA 6000 Nano kit (Agilent).
500ng of RNA was used to prepare each mRNA library. PolyA+ RNA selected RNA libraries were generated by the LMS Core Genomics Facility using the TruSeq Stranded mRNA Library Prep Kit (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description CD23-iCre_0hrs_2
Genecounts.csv
Data processing Illumina CASAVA 1.8.4 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using tophat2 (2.0.11) with default settings.
Gene annotations were obtained from Ensembl Mouse genome (NCBIM37). Gene-based read count were obtained using featureCounts function from Rsubread Bioconductor package.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Genecounts.csv: Comma-separated text file includes gene counts for each Sample; raw counts of sequencing reads for genes.
 
Submission date Dec 04, 2020
Last update date Sep 30, 2021
Contact name LMS Bioinformatics Core
E-mail(s) bioinformatics@lms.mrc.ac.uk
Organization name MRC London Institute of Medical Sciences
Department Bioinformatics Core
Street address Hammersmith Hospital Campus, Du Cane Road
City London
ZIP/Postal code W12 0NN
Country United Kingdom
 
Platform ID GPL17021
Series (2)
GSE162702 RNAseq of Runx1 ck/o B cells at the resting B cell stage and after 3 hours of activation with anti-IgM
GSE162704 RUNX1 controls the rate of cell cycle entry during naive B cell activation by regulating expression of cell cycle and immunomodulatory genes in response to BCR stimulation
Relations
BioSample SAMN17004649
SRA SRX9633948

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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