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| Status |
Public on Nov 17, 2014 |
| Title |
DDX21 iCLIP Biological replicate 2 |
| Sample type |
SRA |
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| Source name |
HEK293 Cells
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| 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
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| Growth protocol |
HEK293 were grown under standard tissue culture conditions
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| 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)
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
iCLIP-seq protocol
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| 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.
DDX21_iCLIPseq_RTstops.bw = bigWig file of high confidence RT stops from merged biological replicates of DDX21 iCLIPseq. Located on series entry.
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
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| 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 |
GPL18573 |
| Series (1) |
| GSE56802 |
RNA helicase DDX21 coordinates transcription and noncoding RNA processing of the ribosomal pathway |
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| Relations |
| BioSample |
SAMN02727887 |
| SRA |
SRX952175 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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