|
| Status |
Public on Feb 16, 2012 |
| Title |
Hela_hnRNPU_CLIP_rep2 |
| 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 HiSeq 2000 |
| |
|
| Description |
library from hnRNP U-RNA complex
|
| Data processing |
Hela_hnRNPU_CLIP_rep2.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 |
GPL11154 |
| Series (1) |
| GSE34491 |
Nuclear Matrix Factor hnRNP U/SAF-A Exerts a Global Control of Alternative Splicing by Regulating U2 snRNP Maturation |
|
| Relations |
| SRA |
SRX111919 |
| BioSample |
SAMN00766231 |
