|
Status |
Public on Dec 01, 2019 |
Title |
sh_0.5h |
Sample type |
SRA |
|
|
Source name |
HeLa-S3 cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: HeLa expression: Brd4 shRNA uv treatment: 0.5h
|
Treatment protocol |
HeLaS3 cells stable expressing Ctrl shRNA and Brd4 shRNA were treated with 60 J/cm2 ultraviolet (UV) light. The cells were collected at 0.5, 1 and 2 hr after UV treatment, and Trizol was added for total RNA extraction. Then the sample was treated with DNase I (Ambion) to remove any potential contaminating DNA.
|
Growth protocol |
HeLa-S3 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin (Invitrogen). The cells were maintained in a 5% CO2 humidified incubator at 37°C.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA extraction was extracted with Trizol reagent. RNA libraries performed by WuXi AppTec and Ribobio.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina MiSeq |
|
|
Description |
Brd4 knock down cells treatment for 0.5 hours
|
Data processing |
Illumina Casava1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The number of raw reads mapped to genes was calculated by RSEM(rsem-1.2.4), the reference genome using hg19, then put all the samples results together and normalized by EDAseq(1.99.1), genes expression fold change were calculated using normalized raw reads. Genome_build: hg19 Supplementary_files_format_and_content: Each files contain Rsem output, including raw reads, TPM and RPKM, one extra file contains all the samples expression value after normalized.
|
|
|
Submission date |
Nov 17, 2014 |
Last update date |
Dec 01, 2019 |
Contact name |
Lihui Lin |
E-mail(s) |
lin_lihui@gibh.ac.cn
|
Phone |
020-32015291
|
Organization name |
Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science
|
Department |
Stem cell
|
Lab |
Pei Duanqing
|
Street address |
No.190, Kaiyuan Street
|
City |
Guangzhou |
State/province |
Guangdong |
ZIP/Postal code |
GD20 |
Country |
China |
|
|
Platform ID |
GPL15520 |
Series (1) |
GSE63385 |
UV Stress Regulates Differential Associations of Brd4 and P-TEFb with Chromatin and Modulates Transcription by Brd4 Acting as either Activator or Repressor |
|
Relations |
BioSample |
SAMN03199331 |
SRA |
SRX761640 |