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Sample GSM1819209 Query DataSets for GSM1819209
Status Public on Apr 21, 2016
Title DDX3 R534H Ars iCLIP 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
flag-tagged protein: DDX3 R534H
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_R534_Ars_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 SAMN03855818
SRA SRX1092004

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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