|
| Status |
Public on Apr 21, 2016 |
| Title |
DDX3 WT iCLIP rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Embryonic kidney
cell line: HEK293-Flp-In-T-Rex
gender: female
treatment: control
flag-tagged protein: DDX3 WT
rip antibody: anti-FLAG (Sigma, catalog# F1804, lot# SLBF6631) then anti-DDX3 (Abcam, catalog# ab37160, lot# GR57731-4 ) antibody
|
| Treatment protocol |
Cells were UV crosslinked at 254nm for 0.3J/cm^2 to in vivo fix RNA-RBP interactions
|
| Growth protocol |
HEK293 cells were grown under standard serum conditions and FLAG-tagged DDX3 variant expression (FLAG-DDX3 WT or R534H) was induced with doxycycline
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lysates were clarified from sonicated HEK293 and DDX3-RNA complexes were isolated first with anti-FLAG (Sigma, A2220) then anti-DDX3 (Abcam, ab37160) antibody.
Libraries were prepared according to the FAST-iCLIP protocol (PMID: 25411354)
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Protein enriched RNA
DDX3_WT_iCLIP.bw
|
| Data processing |
library strategy: iCLIP-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
RT stop identificaiton, gene assignment, and peak calling was performed as in FAST-iCLIP (PMID: 25411354)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file containing unique RT stops from the high confidence intersection of biological replicates of DDX3 iCLIP
|
| |
|
| 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) |
| GSE70801 |
Profile of RNAs bound by wild-type (WT) or R534H variant of DDX3 with or without Sodium Arsenite treatment [iCLIP-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 |
SAMN03855825 |
| SRA |
SRX1092011 |
