|
| Status |
Public on Sep 30, 2021 |
| Title |
Runx1-KO rep1 - restingB (0hrs) |
| Sample type |
SRA |
| |
|
| Source name |
spleen
|
| Organism |
Mus musculus |
| Characteristics |
genotype: CD23iCre/Runx1 ck/o
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 |
Runx1-KO_0hrs_1
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 |
SAMN17004643 |
| SRA |
SRX9633953 |
