|
| Status |
Public on Jan 03, 2013 |
| Title |
3T3-2hrs-severe-HS-RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
3T3 cells
|
| Organism |
Mus musculus |
| Characteristics |
treatment: severe heat shock
cell line: 3T3 cells
assay type: polyA selected RNA
|
| Treatment protocol |
Mild HS: 8 hours in 42 deg C, Severe HS: 2 hours in 44 deg C.
|
| Growth protocol |
DMEM+10%FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAseq- RNAeasy for RNA extraction and standard illumina PE including size selection. Riboseq - RNA extraction and library prepration as described in Ingolia et al. Science, 2009
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
RNAseq: mapping was performed using bowtie v. 12.3 with the following parameters: "-m 1 --best --strata -m 1 -n 2 --best --strata --sam" with a sam format output. reads were uniquely mapped to the mm9 genome, with the addition of splice junctions and ribosomal RNA. the 2 ends of each library were further combined to a single sam file. RNA Seq bowtie files for the combined replicates of control, HS8M, and HS2S are provided as supplementary files on the Series record.
|
| |
|
| Submission date |
Sep 12, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Reut Shalgi |
| E-mail(s) |
reutshalgi@technion.ac.il
|
| Organization name |
Technion
|
| Department |
Faculty of Medicine
|
| Street address |
1 Efron st.
|
| City |
Haifa |
| ZIP/Postal code |
31096 |
| Country |
Israel |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE32060 |
Widespread regulation of translation by elongation pausing in heat shock |
|
| Relations |
| SRA |
SRX217955 |
| BioSample |
SAMN01888279 |
