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| Status |
Public on Jan 15, 2013 |
| Title |
3T3-Hsp70_inhibitor_3hr |
| Sample type |
SRA |
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| Source name |
3T3 cells
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| Organism |
Mus musculus |
| Characteristics |
cell line: 3T3 cells
treatment: Hsp70 inhibitor (VER-155008, Massey et al.) for 3 hours
assay type: Riboseq
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| Treatment protocol |
293T cells were transfected with GFP or Hspa1a plasmid. 48 hours later, cells were either treated with 2 hours of severe heat shock at 44C (HS) or not.
Hsp70 inhibitor: VER-155008 (Massey et al. 2010) at 20microM concentration for 3 hours.
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| Growth protocol |
DMEM+10%FBS
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| Extracted molecule |
total RNA |
| Extraction protocol |
Riboseq - described in Shalgi et al. 2013. similar to Ingolia et al. Science, 2009
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Riboseq: first, reads were trimmed to a length of 32, then polyAs were further trimmed off. reads with lengthes of 22-32 (for the Hsp70 inhibitor sample, 28-32 were used) were seperately uniquely mapped to the same genome file using bowtie, and the output sam files were unified to create a single sam file for each sample.
Genome_build: mm9 and hg18
Supplementary_files_format_and_content: BED files
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| Submission date |
Jan 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Reut Shalgi |
| E-mail(s) |
[email protected]
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| Organization name |
Technion
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| Department |
Faculty of Medicine
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| Street address |
1 Efron st.
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| City |
Haifa |
| ZIP/Postal code |
31096 |
| Country |
Israel |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE32060 |
Widespread regulation of translation by elongation pausing in heat shock |
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| Relations |
| SRA |
SRX217027 |
| BioSample |
SAMN01886422 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1063574_Hsp70_inhibitor_3hr_fp.fastq.bed.gz |
226.8 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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