|
| Status |
Public on Oct 16, 2012 |
| Title |
HeLa-siTUTs-1 |
| Sample type |
SRA |
| |
|
| Source name |
Cervical cancer cells transfected with siRNAs against TUT7, TUT4, and TUT2 two times over a 4~5 day period (rep 1).
|
| Organism |
Homo sapiens |
| Characteristics |
transfection: siTUTs
cell line: HeLa
|
| Treatment protocol |
HeLa cells were transfected with 42nM of siLuciferase or 14nM of each siTUT7, 4, and 2 or GFP using Lipofectamine 2000 (Invitrogen). Transfection was performed two times over a 4~5 day period to enhance knockdown efficiency.
|
| Growth protocol |
HeLa cells were grown in DMEM supplemented with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To prepare small RNA cDNA libraries, total RNAs were separated on 15% urea-PAGE and 17~30nt RNAs were gel-purified. Size fractionized RNAs were ligated with 3' adapter using T4 RNA ligase2 trucated form (NEB). 3’ adaptor-ligated mixture was hybridized with RT primer (NEB v1.5). After RT primer hybridization, RT primer hybridized mixture was ligated with 5' adapter using T4 RNA ligase1 (NEB). The ligation products were reverse transcribed using superscript II (Invitrogen) and the cDNA was PCR-amplified with Phusion DNA polymerase (NEB).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
small RNA
|
| Data processing |
All small RNA sequences except low-quality reads are provided with the number of reads for each unique sequence. Illumina SRA v1.5 3' adapter sequences are trimmed using half-open Smith-Waterman algorithm (score parameters: 2 for match, -2 for mismatch, -3 for linear gap penalty).
|
| |
|
| Submission date |
Feb 15, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Hyeshik Chang |
| E-mail(s) |
hyeshik@snu.ac.kr
|
| Organization name |
Seoul National University
|
| Department |
School of Biological Sciences
|
| Lab |
Hyeshik Chang Lab
|
| Street address |
Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu
|
| City |
Seoul |
| State/province |
South Korea |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE35835 |
Small RNA profiles following TUT knock-down in HeLa |
| GSE40236 |
Small RNA and mRNA profiles following TUT knock-down in HeLa |
|
| Relations |
| SRA |
SRX120056 |
| BioSample |
SAMN00790459 |
