|
| Status |
Public on Jun 07, 2016 |
| Title |
MDA-RPF-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-parental
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-parental
rep: 1
fraction: RPF
|
| Treatment protocol |
Cells were treated 0.1mg/ml cycloheximide
|
| Growth protocol |
Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted post treatment per manufacturer's instructions
Samples were prepared for sequencing per manufacturer's instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ribosome footprinting
|
| Data processing |
FASTQ reads were quality trimmed and subjected to adapter removal (cutadapt). The trimmed sequences were then mapped against contaminating RNAs (i.e. rRNA and tRNA sequences) using Bowtie2. Unaligned reads were then aligned to the human transcriptome using Tophat2.
Cufflinks and cuffdiff were used to normalize ribosome protected fragments (RPF) to total RNA (TT) prepared in parallel.
The difference between RPF to TT log fold-change for each sample was used as a measure of ribosome occupancy.
Genome_build: hg19
Supplementary_files_format_and_content: cufflinks tracking output file for transcript isoforms
|
| |
|
| Submission date |
Jan 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Hani Goodarzi |
| Organization name |
UCSF
|
| Department |
Biochemistry and Biophysics
|
| Street address |
600 16th St, GH S312D
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE77315 |
Ribosomal footprinting of MDA-Parental and MDA-LM2 |
| GSE77401 |
Modulated expression of specific tRNA species drives cancer progression |
|
| Relations |
| BioSample |
SAMN04445127 |
| SRA |
SRX1550084 |
