Status
Public on Jan 03, 2013
Title
3T3-2hrs-severe-HS-Riboseq-rep2
Sample type
SRA
Source name
3T3 cells
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
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.
Submission date
Sep 12, 2011
Last update date
May 15, 2019
Contact name
Reut Shalgi
Organization name
Technion
Department
Faculty of Medicine
Street address
1 Efron st.
City
Haifa
ZIP/Postal code
31096
Country
Israel
Series (1)
GSE32060
Widespread regulation of translation by elongation pausing in heat shock
Relations
Supplementary file
Size
Download
File type/resource
GSM794859_HS2S_fp_rep2.bowtie.sam.gz
675.3 Mb
(ftp) (http)
SAM
Raw data are available in SRA
Processed data provided as supplementary file