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Sample GSM794860 Query DataSets for GSM794860
Status Public on Jan 03, 2013
Title 3T3-8hrs-mild-2hrs-severe-HS-Riboseq
Sample type SRA
Source name 3T3 cells
Organism Mus musculus
Characteristics treatment: mild followed by 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
Platform ID GPL13112
Series (1)
GSE32060 Widespread regulation of translation by elongation pausing in heat shock
SRA SRX217962
BioSample SAMN01888286

Supplementary file Size Download File type/resource
GSM794860_HS8M2S_fp.bowtie.sam.gz 997.1 Mb (ftp)(http) SAM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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