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Sample GSM1520219 Query DataSets for GSM1520219
Status Public on Feb 13, 2015
Title HuR KO_Ex vivo2 [Ribo-Seq]
Sample type SRA
 
Source name Splenic B cells
Organism Mus musculus
Characteristics strain: HuRflox/flox x mb1cre
genotype: HuR KO
cell isolation: Splenic B cells negative selection using a cocktail of biotin-conjugated antibodies against CD43, CD4 , and Ter-119 (Mylteni 130-090-862)
condition: Ex-vivo
scriptminer index: CTTGTA
Treatment protocol After isolation, splenic B cells were cultured in RPMI 1640 Medium (Dutch Modification) plus 5% FCS, antibiotics, 2 mM L-glutamine and Beta-mercaptoethanol (5 microMolar) at a density of 5x10^5 cells/ml. They were activated with LPS (10 micrograms/ml) for 48 hours.
Growth protocol HuRflox/flox x mb1wt and HuRflox/flox x mb1cre mice were littermates. This mouse line was maintained under Babraham Institute AWEEC and UK home Office regulation.
Extracted molecule cytoplasmic RNA
Extraction protocol ARTseq™ Ribosome Profiling Kit - Mammalian (Epicentre, RPHMR12126)
ARTseq™ Ribosome Profiling Kit - Mammalian (Epicentre, RPHMR12126). ScriptMiner™ Index PCR Primers used for sample multiplexing (Epicentre, Cat. No. SMIP2124)
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 1000
 
Data processing Raw sequence reads were trimmed to remove both barcodes and adapters using Trim Galore (www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (v0.3.3, default parameters).
Remaining sequences were mapped to the mouse GRCm38 genome using Tophat (Bioinformatics. 2009 May 1;25(9):1105-11. and http://ccb.jhu.edu/software/tophat/index.shtml). Read counting was performed using HTSeq. Ensembl annotation GRCm38.72 was used.
Differential gene expression analysis was performed using DESeq2 (Love MI, Huber W and Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2.” bioRxiv). Ensembl annotation GRCm38.72 was used for differential analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: Files contain the report generated by DESeq2 after differential expression analysis.
 
Submission date Oct 07, 2014
Last update date May 15, 2019
Contact name Felix Krueger
E-mail(s) fkrueger@altoslabs.com
Organization name Altos Labs
Department Bioinformatics
Street address Granta Park
City Cambridge
ZIP/Postal code CB21 6GP
Country United Kingdom
 
Platform ID GPL15103
Series (2)
GSE62134 HuR- dependent regulation of mRNA splicing is essential for the B cell antibody response [Ribo-Seq]
GSE62148 HuR- dependent regulation of mRNA splicing is essential for the B cell antibody response
Relations
BioSample SAMN03098054
SRA SRX726850

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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