|
| Status |
Public on Oct 17, 2016 |
| Title |
RNA-seq for BRD4 wild type cells |
| Sample type |
SRA |
| |
|
| Source name |
PEO1 ovarian cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
experiment type: RNAseq
treatment: BRD4.WT
|
| Treatment protocol |
PEO1 cells were treated with or without 200 nM JQ1 for 72 hours or PEO1 cells were infected with lentivirus encoding short hairpin RNA to the human BRD4 gene (shBRD4) or control
|
| Growth protocol |
Human ovarian cancer cell line PEO1 were cultured in RPMI1640 medium (Corning) supplemented with 10% fetal bovine serum (FBS; Sigma), 100 U/ml penicillin and 100 mg/ml streptomycin. Cells were passaged every 3-4 days to complete growth medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol
The sequencing libraries were generated using the Lexogen QuantSeq 3’ mRNA sequencing library preparation kit (SKU:015.24) for Illumina sequencing platform compatible libraries. All 12 libraries were pooled in equal molar amounts and run on the Illumina Nextseq500 using the Mid Output V2 (150 cycles) kit (cat # FC-404-2001)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-seq for BRD4 wild type cells
|
| Data processing |
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 was used for differentail expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed file contains raw counts for all genes
|
| |
|
| Submission date |
May 20, 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) |
| GSE81698 |
Epigenetic targeting of immunocheckpoint PD-L1 by BET bromodomain inhibition |
|
| Relations |
| BioSample |
SAMN05157063 |
| SRA |
SRX1787037 |
