|
| Status |
Public on Jun 01, 2016 |
| Title |
Cells_T47D_siFOXA1_R5020_12 Hours_RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: ER+/PR+ cell models
cell line: T47D
er/pr status: ER+/PR+
drug treatment: 10 nM R5020
hormone exposure time: 12 hours
|
| Treatment protocol |
Steroid-deprived cell models were treated with 10 nM estradiol, 10 nM R5020 or 10 nM of both the hormones for 12 hours.
|
| Growth protocol |
Cell models RNA-seq: Cells were cultured for 48 hours in charcoal-stripped serum media to deprive them of steroids.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Hormone-treated cells were homogenized and total RNA was extracted using Qiagen RNAeasy kit
PolyA tail selection was performed on 250 ng of total RNA. RNA-seq libraries were prepared using NEBNext kit.
Details of library preparation strategy are provided in the materials and methods section (RNA expression and RNA-sequencing) of the paper.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
mRNA-seq (knockdown)
Processed data file: T47D_siFOXA1_annotated100kb.csv
|
| Data processing |
The FASTQ files were filtered and good quality reads were groomed and subsequently aligned to HG19 genome build using TopHat.
Relative expression of transcripts were calculated by subjecting TopHat output (BAM files) to Cufflinks package.
Cufflinks assemblies obtained from Cufflinks package were merged using cuffmerge. For every model system, cufflink assemblies of each of the treatments were merged with the cufflinks assemblies of the respective vehicle-treated samples.
The output from Cuffmerge along with the corresponding TopHat output (BAM files) were subjected to Cuffdiff to calculate transcript expression.
Genes that were up or down regulated by at least two fold were used for downstream analyses.
Genome_build: HG19
Supplementary_files_format_and_content: CSV includes RPKM values for each each of the treatment conditions (E2, R5020 or E2+R5020) versus control treatment. Union of all estrogen and progestin-regulated genes for the respective samples is provided.
|
| |
|
| Submission date |
Apr 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Hari Singhal |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Chicago
|
| Department |
Ben May Department for Cancer Research
|
| Lab |
Geoffrey L Greene
|
| Street address |
929 E 57th St
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE80098 |
Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer. |
| GSE80366 |
Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer. [cell models RNA-seq] |
|
| Relations |
| BioSample |
SAMN04631288 |
| SRA |
SRX1688781 |
