|
Status |
Public on Oct 01, 2012 |
Title |
direct RNA sequencing (DRS) of control HeLa cells |
Sample type |
SRA |
|
|
Source name |
HeLa
|
Organism |
Homo sapiens |
Characteristics |
strategy: RNA-Seq cell line: HeLa genotype/variation: control
|
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.
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|
|
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
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|
|
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 |
SRX186539 |
BioSample |
SAMN01173956 |