|
| 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 |
| 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 |
SAMN02940605 |
| SRA |
SRX661224 |
