|
| Status |
Public on May 08, 2018 |
| Title |
shctr_CIT (Rep 2) |
| Sample type |
SRA |
| |
|
| Source name |
shctr_CIT, CH12
|
| Organism |
Mus musculus |
| Characteristics |
cell line: CH12
cell type: B-cell lymphoma
genotype/variation: control
culture condition: CIT
|
| Treatment protocol |
Cells were cultured in unstimulated (UNS) or anti-CD40, IL-4 and TGF-β (CIT) stimulation conditions for 24h.
|
| Growth protocol |
CH12 cells were stably depleted of Ddx1 using lentivirus expressing short-hairpin RNA (shDdx1). CH12 cells transduced with a shRNA sequence that does not target any known mammalian mRNA (shCtrl) were used as a control.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclear RNA was fractionated in nucleoplasmic and chromatin fractions.
Chromatin-associated RNA was depleted for rRNA using the Ribo-Zero Magnetic kit (Illumina). Libraries were prepared using the NEBNext Ultra Directional RNA Library Prep kit and NEBnext multiplex Oligos (Index Primers Set 2) for Illumina (NEB).
RNA-Seq on a HiSeq 4000 sequencer (Illumina) with 75 bp paired-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
75-bp paired-end HiSeq 4000 sequencing reads were aligned to the mouse genome (mm10) using BWA with default parameters.
Prior to alignment, adaptor sequences were trimmed using Cutadapt retaining reads longer than 10 bases.
Uniquely aligned reads with no more than two mismatches were kept for further analysis.
Data were scaled to library size. Bigwig track files were generated using UCSC bedGraphToBigWig tool.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig file containing read densities from RNA-seq experiments.
|
| |
|
| Submission date |
Mar 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicholas Proudfoot |
| E-mail(s) |
nicholas.proudfoot@path.ox.ac.uk
|
| Organization name |
Sir William Dunn School of Pathology, University of Oxford
|
| Street address |
South Parks Road
|
| City |
Oxford |
| ZIP/Postal code |
OX1 3RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE95635 |
RNA Helicase DDX1 Converts RNA G-Quadruplex Structures into R-Loops to Promote IgH Class Switch Recombination |
|
| Relations |
| BioSample |
SAMN06470232 |
| SRA |
SRX2610306 |
