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Sample GSM1446086 Query DataSets for GSM1446086
Status Public on Nov 17, 2014
Title DDX21_SAT mutant iCLIP Biological replicate 1
Sample type SRA
Source name HEK293 Cells
Organism Homo sapiens
Characteristics cell line: HEK293
cell type: embryonic kidney
genotype/variation: SAT mutant
Treatment protocol HEK293 cells were transduced with a doxycycline inducible FH-DDX21_SAT mutant construct. Before assaying cells were treated with 0.25ug/mL doxycycline for 24 hours to express the FH-DDX21_SAT. Cells were then processed for iCLIP under previously described conditions (PMID: 24184352)
Growth protocol HEK293 were grown under standard tissue culture conditions
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated HEK293 and DDX21_SAT-RNA complexes were isolated with anti-Flag and anti-HA antibodies.
Libraries were prepared according to the standard iCLIP protocol (PMID: 24184352). Each sequencing read conatins a 13 nt random (D's and N's) and experimental (XXXX) "DDDNNXXXXNNNN". The experimental barcodes are described in (PMID: 24184352)
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
Description iCLIPseq
Data processing Barcodes and adaptor sequences were trimmed and iCLIPseq reads were aligned to hg19 using bowtie as previously described (PMID: 24184352). Crosslinked nucleotides were identified as the first base of each trimmed read.
Crosslinked nucleotides were only analyzed if present at least twice in both biological replicates.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig : the bigWig file provided contains processed Crosslinked nucleotides from the DDX21_SAT iCLIP experiment. Data presented is an intersection of the two biological replicates
Submission date Jul 25, 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 GPL16791
Series (1)
GSE56802 RNA helicase DDX21 coordinates transcription and noncoding RNA processing of the ribosomal pathway
BioSample SAMN02940605
SRA SRX661224

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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