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Status |
Public on Jan 03, 2013 |
Title |
3T3-2hrs-severe-HS-Riboseq-rep2 |
Sample type |
SRA |
|
|
Source name |
3T3 cells
|
Organism |
Mus musculus |
Characteristics |
treatment: severe heat shock cell line: 3T3 cells assay type: Riboseq
|
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
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2000 |
|
|
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.
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|
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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 |
GPL13112 |
Series (1) |
GSE32060 |
Widespread regulation of translation by elongation pausing in heat shock |
|
Relations |
SRA |
SRX217961 |
BioSample |
SAMN01888285 |