|
| Status |
Public on Apr 21, 2016 |
| Title |
DDX3 R534H ribosome profiling with sodium arsenite rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Embryonic kidney
cell line: HEK293-Flp-In-T-Rex
gender: female
treatment: sodium arsenite
expressed protein: DDX3 R534H
|
| Treatment protocol |
Cells were treated with or without 0.5 mM sodium arsenite for 45 minutes.
|
| Growth protocol |
HEK293 cells were grown under standard serum conditions and FLAG-tagged Renilla luciferease (Rluc) control, DDX3 WT, or DDX3 R534H expression was induced by doxycycline addition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lysates were treated with RNase I, ribosomes were collected, ribosomal RNAs were depleted with Ribo-Zero kit (EpiCentre), and ribosome-protected mRNA fragments were enriched.
Libraries were prepared according to the ribosome profiling protocol (PMID: 19213877) and ARTseqTM Ribosome Profiling Kit protocol (EpiCentre).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Ribosome-protected mRNA fragments
Ribosome profiling
|
| Data processing |
library strategy: Ribo-seq
Sequencing reads were trimmed of 3' adaptors, collapsed for PCR duplicates, stripped of the 5' barcode, and mapped to the human (hg19) genome using bowtie2
Gene assignment, and peak calling was performed as in ribosome profling (PMID: 19213877)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file containing unique ribosome-protected mRNA fragments for each replicate
|
| |
|
| Submission date |
Jul 11, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Sekyung Oh |
| E-mail(s) |
ohskjhmi@gmail.com
|
| Phone |
650-725-3354
|
| Organization name |
Stanford University School of Medicine
|
| Department |
Neurology and Neurological Sciences
|
| Street address |
1201 Welch Road, MSLS P224
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE70802 |
Profiles of ribosome-associated mRNAs regulated by expression of wild-type (WT) or R534H variant of DDX3 with or without Sodium Arsenite treatment [Ribo-Seq] |
| GSE70804 |
Profiles of ribosome-associated mRNAs regulated by expression of wild-type (WT) or R534H variant of DDX3 with or without Sodium Arsenite treatment |
|
| Relations |
| BioSample |
SAMN03855831 |
| SRA |
SRX1092017 |
