|
| Status |
Public on Oct 13, 2021 |
| Title |
RNAseq PARP-1 KD E2 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
human Estrogen receptor alpha+ breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
genotype/variation: PARP-1 KD
treatment: 100 nM E2
|
| Treatment protocol |
Prior to all experiments, MCF-7 cells were grown for 3 days in phenol red-free MEM Eagle medium supplemented with 5% charcoal-dextran-treated calf serum (CDCS). For experiments, cells were treated with 100 nM E2 or vehicle (ethanol) for 3 hours.
|
| Growth protocol |
MCF-7 cells were kindly provided by Benita S. Katzenellenbogen (University of Illinois, Urbana-Champaign) used for the genomic. MCF-7 cells were maintained in Minimum Essential Medium Eagle supplemented with 5% calf serum (CS).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
MCF-7 cells with shRNA-mediated knockdown of luciferase (Luc; as a control) or PARP-1 were isolated and subjected to RNA-seq as described previously (PMID: 21807852, PMID: 26236012).
Estrogen-withdrawn MCF-7 cells were treated with ethanol or 100 nM E2 for 3 hours. Total RNA was isolated MCF-7 cells using the RNeasy kit (Qiagen, 74136) according to the manufacturer’s instructions. The RNA collected was processed for whole transcriptome polyadenylated RNA sequencing (polyA+ RNA-seq).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNAseq_PARP-1_KD_E2_Plus.bw, RNAseq_PARP-1_KD_E2_Minus.bw
|
| Data processing |
Quality control for the RNA-seq data was performed using the FastQC tool
The reads were then mapped to the human reference genome (GRCh37/hg19) with previously described comprehensive gene annotation using the default parameters in Tophat (v2.0.12) (PMID: 19289445)
Differences in gene expression between RNA-seq datasets were calculated using the cufflinks suite with a statistical threshold of FDR, 0.05 (PMID: 20436464). Gene expression changes were measured by the fold change in each of the treatments and were visualized as box and whisker plots.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
May 06, 2021 |
| Last update date |
Oct 13, 2021 |
| Contact name |
W. Lee Kraus |
| E-mail(s) |
[email protected]
|
| Organization name |
UT Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd.
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-8511 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE173976 |
The role of PARP-1 in estrogen-dependent transcription [RNA-seq] |
| GSE173981 |
The role of PARP-1 in estrogen-dependent transcription |
|
| Relations |
| BioSample |
SAMN19035371 |
| SRA |
SRX10808276 |
