|
| Status |
Public on Feb 05, 2017 |
| Title |
RNA-seq for JQ1-treated cells |
| Sample type |
SRA |
| |
|
| Source name |
JQ1-treated cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: OVCAR3
agent: JQ1
|
| Treatment protocol |
cells were incubated with 0.5 mM ethidium uridine (EU) and treated with 125 nM JQ1 for 40min
|
| Growth protocol |
Ovarian cancer cell lines were cultured in RPMI1640 medium (Corning) supplemented with 10% fetal bovine serum (FBS; Sigma), 100 U/ml penicillin, 100 ug/ml streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA isolated using Trizol reagent
Ovation Human FFPE RNA-Seq Multiplex System 1-8 (Nugen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-seq for JQ1-treated cells
|
| Data processing |
Chip-seq files were aligned using bowtie version 0.12.9 to human genome hg19
Peak calling was done with homer (v1.0) software with options -fdr 0.01 -style histone
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and Hg19 genome with UCSC known gene set.
edgeR was used for differential expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq processed files contain Homer peak calling output; RNA-Seq expression file contains raw counts and FPKM values for all genes
|
| |
|
| Submission date |
Feb 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Priyankara J Wickramasinghe |
| E-mail(s) |
priyaw@wistar.org
|
| Phone |
2154956837
|
| Organization name |
The Wistar Institute
|
| Department |
Bioinformatics
|
| Lab |
Genomics
|
| Street address |
3601 Spruce Street
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE77568 |
Inhibition of BET protein BRD4 activity synergizes with cisplatin in ovarian cancer by targeting ALDH activity through an ALDH1A1 super-enhancer and the associated enhancer RNA |
|
| Relations |
| BioSample |
SAMN04455974 |
| SRA |
SRX1560788 |
