|
| Status |
Public on May 15, 2013 |
| Title |
Roquin_IP3 |
| Sample type |
SRA |
| |
|
| Source name |
RAW264.7_Roquin_IP
|
| Organism |
Mus musculus |
| Characteristics |
cell line: RAW264.7
ip antibody/beads information: rabbit polyclonal, Bethyl, 514A and 515A plus protein A/G beads
molecule subtype: RNA purified from Roquin IP
|
| Treatment protocol |
RAW264.7 cells were treated with LPS (100 ng/ml, Sigma, L2630, E. coli serotype O111:B4) for 2 h.
|
| Growth protocol |
RAW264.7 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (PAA Laboratories), 2 mM L-glutamine, 100 U/ml penicillin and 0.1 mg/ml streptomycin (all PAN Biotech) at 37°C in 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were mechanically disrupted using a tissue lyser. RNA was isolated before (Input) or after IP (ctrl IP or Roquin IP) with TriFast reagent.
RNA libraries were prepared for sequencing using the TruSeq RNA Sample Preparation Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 3
|
| Data processing |
Basecalling with CASAVA v1.8.2
Mapping to the mouse genome NCBI build 37 with BWA.
Reads were summarized for gene models with the Bioconductor package easyRNASeq v1.2.5. The exon coordinates of RefSeq annotated mRNAs were obtained from the refGene table of the UCSC genome browser.
Differential abundance was tested for with the Bioconductor package DESeq v1.8.3.
Genome_build: NCBI build 37
Supplementary_files_format_and_content: The 'RoquinIP_processed.txt' file contains, for each sample, the count table obtained with easyRNASeq, the fold changes and the p-values computed with DESeq.
|
| |
|
| Submission date |
Mar 01, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Georg Stoecklin |
| E-mail(s) |
[email protected]
|
| Organization name |
German Cancer Research Center
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE44775 |
Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs. |
|
| Relations |
| SRA |
SRX248294 |
| BioSample |
SAMN01974594 |
