|
Status |
Public on Nov 17, 2014 |
Title |
DDX21_SAT mutant iCLIP Biological replicate 2 |
Sample type |
SRA |
|
|
Source name |
HEK293 Cels
|
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)
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|
|
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
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|
|
Submission date |
Jul 25, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Ryan Alexander Flynn |
E-mail(s) |
raflynn@stanford.edu
|
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 |
|
Relations |
BioSample |
SAMN02940606 |
SRA |
SRX661225 |