|
| Status |
Public on Oct 16, 2012 |
| Title |
HeLa-siTUTs (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
Cervical cancer cells transfected with siRNA against luciferase two times over a 5 day period.
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
sirna: siTUTs
treatment: transfected with 14nM of each siTUT7
|
| Treatment protocol |
HeLa cells were transfected with 42nM of siLuciferase or 14nM of each siTUT7, 4, and 2 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 |
polyA RNA |
| Extraction protocol |
To prepare mRNA libraries, mRNAs were purified from total RNAs using Dynabeads mRNA Purification Kit (Invitrogen, 61011). Purified mRNAs were fragmented by RNA Fragmentation Reagents (Ambion, AM8740). After fragmentation, phosphate group at 3′ end was removed by Antarctic phosphatase (NEB, M0289L), and RNAs were 5′ phosphorylated by T4 PNK (NEB). Directional and multiplexed mRNA libraries were generated using TruSeq Small RNA Sample Preparation Kit (Illumina, RS-200–0012). The mRNA libraries were sequenced using Illumina HiSeq 2000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were mapped, measured and quantifed by cufflinks v2.0.0, tophat v2.0.0 and bowtie v2.0.0-beta5 with --library-type fr-secondstrand and other default options. The gene annotations for cufflinks were retrieved from Illumina iGenome repository as of Sep 11, 2011.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and log2 fold changes between samples
|
| |
|
| Submission date |
Aug 20, 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 |
GPL11154 |
| Series (2) |
| GSE40228 |
mRNA profiles following TUT knock-down in HeLa |
| GSE40236 |
Small RNA and mRNA profiles following TUT knock-down in HeLa |
|
| Relations |
| SRA |
SRX179485 |
| BioSample |
SAMN01121068 |
