|
| Status |
Public on May 18, 2017 |
| Title |
48h 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 |
SAMN03701907 |
| SRA |
SRX1033336 |
