|
| Status |
Public on Oct 01, 2012 |
| Title |
direct RNA sequencing (DRS) of CstF64-RNAi cells |
| Sample type |
SRA |
| |
|
| Source name |
Stable HeLa cell line
|
| Organism |
Homo sapiens |
| Characteristics |
strategy: RNA-Seq
cell line: HeLa
genotype/variation: CstF64-RNAi
|
| Treatment protocol |
HeLa cells were transfected with shRNA construct and/or siRNAs using Lipofectamine 2000 (Invitrogen)
|
| Growth protocol |
DMEM + 10% fetal bovine serum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
iCLIP-seq: RNAs were extracted from immunoprecipitated protein-RNA complexes; for direct RNA sequencing, RNAs were extracted from cells using Trizol reagent (Invitrogen)
iCLIP-seq libraries were prepared as described by Konig et al, NSMB (2010) 17: 909; the antibody used was purchased from Bethyl Laboratories (Cat#: A301-092A; lot #: A301-092A-1)
iCLIP-seq library strategy was the same as by Konig et al, NSMB (2010) 17: 909.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Helicos HeliScope |
| |
|
| Data processing |
iCLIP-seq: 1. Raw reads were demultiplexed using the sequencing barcode unique to each replicate and an additional random trinucleotide identifying individual DNA molecules was clipped but kept as metadata; 2. Reads with quality less than 20 for 10% or more of the bases were removed.3. We mapped the remaining reads to build hg19 of the human genome using bowtie
iCLIP-seq reads were mapped to hg19 using Bowtie
Direct RNA sequencing: Reads were filtered and mapped to hg19 using indexDPgenomic tool in Helisphere (www.Helicosbio.com)
Genome_build: hg19
Supplementary_files_format_and_content: bed format
|
| |
|
| Submission date |
Sep 13, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Yongsheng Shi |
| E-mail(s) |
yongshes@uci.edu
|
| Phone |
9498240358
|
| Organization name |
University of California, Irvine
|
| Department |
Microbiology and Molecular Genetics
|
| Street address |
B228 Med Sci I
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL14761 |
| Series (1) |
| GSE40859 |
Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation |
|
| Relations |
| SRA |
SRX186540 |
| BioSample |
SAMN01173957 |
