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Sample GSM1819223 Query DataSets for GSM1819223
Status Public on Apr 21, 2016
Title Rluc control ribosome profiling 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
expressed protein: Rluc control
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 SAMN03855832
SRA SRX1092018

Supplementary file Size Download File type/resource
GSM1819223_R7_Rluc_control_rep_2.hg19.bw 41.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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