|
| Status |
Public on Feb 13, 2015 |
| Title |
HuR KO_Ex vivo1 [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: GATCAG
|
| 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 |
SAMN03098053 |
| SRA |
SRX726849 |
