|
Status |
Public on Feb 16, 2012 |
Title |
Hela_hnRNPU_CLIP_rep1 |
Sample type |
SRA |
|
|
Source name |
HeLa cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: HeLa antibody: monoclonal anti-hnRNP U antibody (3G6)
|
Growth protocol |
HeLa cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) with 10% newborn bovine serum plus 100 U penicillin /streptomycin (Gibico) at 37°C in 5% CO2.
|
Extracted molecule |
total RNA |
Extraction protocol |
HeLa cells were UV-irradiated at 400 mj and collected by scraping the cells from 15-cm plates. hnRNP U immunoprecipitation was done in 1% NP-40 wash buffer. 3' adaptor was first added to the immunoprecipitated hnRNP U-RNA complex on beads, then the eluted protein-RNA complex was subject to 10% Novex NUPAGE gel. After transfering to NC membrane, the corresponding band was cut and RNA was extracted. After 5' adaptor liagtion, RT-PCR was performed by using Super Script III and Ex taq polymerase.
|
|
|
Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina Genome Analyzer II |
|
|
Description |
library from hnRNP U-RNA complex
|
Data processing |
Hela_hnRNPU_CLIP_rep1.bed; genome build: hg18 Library strategy: CLIP-seq After removing 3' adaptor sequence, the tags longer than 20 nt were mapped to the reference human genome (hg18) with Bowtie by allowing maximum 2 mismatches in the first 25 nt, and only tags with less than or equal to 10 mapped locations were kept.
|
|
|
Submission date |
Dec 16, 2011 |
Last update date |
May 15, 2019 |
Contact name |
Xiang-Dong Fu |
Organization name |
UC San Diego
|
Department |
CMM
|
Lab |
George Palade Laboratories
|
Street address |
9500 Gilman Drive, Room 231
|
City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92093-0651 |
Country |
USA |
|
|
Platform ID |
GPL9115 |
Series (1) |
GSE34491 |
Nuclear Matrix Factor hnRNP U/SAF-A Exerts a Global Control of Alternative Splicing by Regulating U2 snRNP Maturation |
|
Relations |
SRA |
SRX111918 |
BioSample |
SAMN00766230 |