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| Status |
Public on Nov 17, 2014 |
| Title |
DDX21-ChIPSeq |
| Sample type |
SRA |
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| Source name |
HEK293 Cells
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| Organism |
Homo sapiens |
| Characteristics |
antibody 1: DDX21, Novus Biologicals, Cat# BP100-1781
antibody 2: DDX21, Novus Biologicals, Cat# NBP1-83310
cell line: HEK293
cell type: embryonic kidney
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| Growth protocol |
HEK293 were grown under standard tissue culture conditions
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated HEK293 nuclei and histone-DNA complexes were isolated with anti-DDX21 antibody.
Libraries were prepared according to NEBNext kit.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
ChIP-seq reads were aligned to the hg19 genome assembly using DNANexus
peaks were called using QuEST with the following setting: ChIP estimate threshold (20),ChIP extension fold enrichment (3), and a ChIP-to-background fold enrichment (3)
Genome_build: hg19
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| Submission date |
Apr 15, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ryan Alexander Flynn |
| E-mail(s) |
raflynn@stanford.edu
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| Organization name |
Stanford University
|
| Street address |
380 Roth Way, Room 265
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE56802 |
RNA helicase DDX21 coordinates transcription and noncoding RNA processing of the ribosomal pathway |
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| Relations |
| BioSample |
SAMN02727889 |
| SRA |
SRX952172 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1369392_DDX21_ChIPseq.bedGraph.gz |
82.4 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM1369392_DDX21_ChIPseq_normalized.wig.gz |
19.7 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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