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Sample GSM1691206 Query DataSets for GSM1691206
Status Public on May 18, 2017
Title 36h ribosome footprint data
Sample type SRA
 
Source name MM1.S cells
Organism Homo sapiens
Characteristics drug treatment: 0.5 nM bortezomib
cell lline: MM1.S
Treatment protocol Cells were treated with 0.5 nM bortezomib
Extracted molecule total RNA
Extraction protocol mRNA-seq and ribosome footprint samples were prepared by the method of Ingolia et al. Cell (2011) 147:789.
mRNA-seq and ribosome footprint sequencing libraries were prepared by the method of Ingolia et al. Cell (2011) 147:789.
mRNA-seq, ribosome profiling
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description ribosome-protected mRNA
Data processing Stranded alignment with Bowtie 0.12.8 to hg19 canonical transcripts allowing up to 2 mismatches
Read counting using in-house C++ scripts based on bowtie alignments, with counting only based on coding sequence of canonical splice isoform per UCSC annotation
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet with raw read counts and RPKM for all reads mapping to canonical coding sequence of hg19-annotated transcripts. Only genes with >128 raw reads mapping to the coding sequence in all samples are included.
 
Submission date May 19, 2015
Last update date May 15, 2019
Contact name Arun P. Wiita
Organization name University of California, San Francisco
Department Laboratory Medicine
Street address 185 Berry St., Suite 290
City San Francisco
State/province CA
ZIP/Postal code 94107
Country USA
 
Platform ID GPL16791
Series (1)
GSE69047 Time-Resolved Proteomics Extends Ribosome Profiling-Based Measurements of Protein Synthesis Dynamics
Relations
BioSample SAMN03701906
SRA SRX1033335

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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