NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1547892 Query DataSets for GSM1547892
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

Supplementary file Size Download File type/resource
GSM1547892_sh_0.5h.genes.results.txt.gz 1.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.