|
| Status |
Public on Feb 16, 2012 |
| Title |
Hela_hnRNPU_RNAseq_knockdown |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
transfection: hnRNP U knockdown
|
| Treatment protocol |
Transfection of siRNA against hnRNP U
|
| 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 |
polyA RNA |
| Extraction protocol |
Total RNAs were extracted by Trizol from treated HeLa cells and polyA RNAs were enriched by oligod(T) selection. After fragmentation, mRNAs were reversely transcribed to cDNA with Superscript II in the presence of random primer. After RNase H digestion, the second strand cDNA was synthesized by DNA pol I followed by adaptor ligation. Size-selected PCR products were sequenced by Illumila Genome Analyzer II.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
hnRNP U knockdown cells
|
| Data processing |
Hela_hnRNPU_RNAseq_knockdown.bed; genome build: hg18
Paired-end reads were separately mapped into a custom Bowtie index, which was built from UCSC knownGenes (hg18) not including introns. Under the constraint of the insert size, only the paired-end reads whose two ends are about 50 nt apart on the same gene were kept. For each pair, the coordinates of the two end reads were mapped back to the genome based on its gene's genomic location, and then joined together. Only the pair-end reads with one unique genomic location 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 |
SRX111921 |
| BioSample |
SAMN00766233 |
