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Sample GSM1369394 Query DataSets for GSM1369394
Status Public on Nov 17, 2014
Title DDX21 iCLIP Biological replicate 1
Sample type SRA
Source name HEK293 Cells
Organism Homo sapiens
Characteristics antibody 1: FLAG-M2, Sigma-Aldrich, Cat# A2220-5ML
antibody 2: HA, Pierce, Cat# 26181
cell line: HEK293
cell type: embryonic kidney
Growth protocol HEK293 were grown under standard tissue culture conditions
Extracted molecule total RNA
Extraction protocol Lysates were clarified from sonicated HEK293 and DDX21-RNA complexes were isolated with anti-Flag and anti-HA antibodies.
Libraries were prepared according to the standard iCLIP protocol (PMID: 24184352)
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina NextSeq 500
Description iCLIP-seq protocol
Data processing Sequencing reads were trimmed of the 3’ adaptor, filtered for quality and length (>20nt insert), PCR duplicates removed, and 5’ adaptor trimmed.
Processed reads were mapped with bowtie2 (parameters –m 1 and –v 2). Mapped reads were collapsed to RT stops as the first nucleotide of each read. RT stops from biological replicates were intersected. Reads passing this filtering were then used for assignment to known protein and noncoding RNAs in hg19. = bigWig file of high confidence RT stops from merged biological replicates of DDX21 iCLIPseq. Located on series entry.
Genome_build: hg19
Submission date Apr 15, 2014
Last update date May 15, 2019
Contact name Ryan Alexander Flynn
Organization name Stanford University
Street address 380 Roth Way, Room 265
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platform ID GPL18573
Series (1)
GSE56802 RNA helicase DDX21 coordinates transcription and noncoding RNA processing of the ribosomal pathway
BioSample SAMN02727888
SRA SRX952174

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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