|
| Status |
Public on Nov 04, 2019 |
| Title |
Riboseq_Ribo_APCdef_shEIF2B5_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
SW480TetOnAPC cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: human colorectal cancer cell line
cell line: SW480TetOnAPC
treatment: EtOH
shRNA: shEIF2B5
|
| Treatment protocol |
SW480TetOnAPC cells were lentivirally infected with an shRNA targeting eIF2B5 or non-specific control (shLuciferase). Cells were treated with 0.5 µg/ml doxycycline or ethanol for 96 hours to restore APC expression.
|
| Growth protocol |
SW480TetOnAPC cells were grown in RPMI 1640 (Sigma). All media were supplemented with 10% FBS (Sigma) and 1% penicillin/streptomycin (Sigma).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ribosomal profiling (Ribo, RPF=ribosome protected fragments) and corresponding RNA-seq were performed using the TruSeq Ribo Profile for Mammalian kit from Illumina according to manufacturer's instructions.
For global gene expression analysis, total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen) including on-column digestion of DNA. Poly-A+ RNA was purified from total RNA with the NEBNextPoly(A) mRNA Magnetic Isolation Module (NEB).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file:
Riboseq_RPF_SW480.txt
|
| Data processing |
Library strategy: Ribo-seq
For Ribo-seq experiments, reads were mapped against the human genome (HG38) using STAR (Dobin et al.) and processed using PRICE (under revision) based on annotations from Ensembl (v86). Briefly, a generative model was fitted per experiment to the observed positions of annotated codons in strongly translated ORFs. This increased signal-to-noise levels from about 3 to more than 5 when mapping reads to codons. Then, translated ORFs were determined by the generalized binomial test built into PRICE using all pooled samples, and each ORF was quantified per experiment using the number of reads mapped to its codons. For the corresponding RNA-seq, reads were mapped against the human genome (HG38) using STAR (Dobin et al.). Then, reads per gene were counted when they were consistent with at least one transcript annotated in Ensembl v86.
genome build: hg38
Supplementary_files_format_and_content: Content of Riboseq_RPF_SW480.txt is described in README.txt. .txt files of the corresponding RNA-seq contain Ensembl gene IDs and non-normalized fractional counts for multimapping genes.
|
| |
|
| Submission date |
Dec 11, 2017 |
| Last update date |
Nov 04, 2019 |
| Contact name |
Martin Eilers |
| Organization name |
University of Wuerzburg
|
| Department |
Chair for Biochemistry and Molecular Biology
|
| Lab |
Martin Eilers
|
| Street address |
Am Hubland
|
| City |
Wuerzburg |
| ZIP/Postal code |
97074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE106858 |
A MYC/GCN2/eIF2alpha negative feedback loop limits protein synthesis to prevent MYC-dependent apoptosis in colorectal cancer |
|
| Relations |
| BioSample |
SAMN08160181 |
| SRA |
SRX3461612 |
