|
| Status |
Public on Jun 01, 2016 |
| Title |
Tumor_N3_E2_48 Hours_RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: ER+/PR- Human tumor explants
er/pr status: ER+/PR-
drug treatment: 10 nM Estradiol
hormone exposure time: 48 Hours
|
| Treatment protocol |
Steroid-deprived tumor explants were treated with 10 nM estradiol, 10 nM R5020 or 10 nM of both the hormones for 24 or 48 hours. Finer details are provided in materials and methods section (Patient tumor explants)
|
| Growth protocol |
Tumor explants: Within one hour of surgery, sliced pieces of tumors were incubated on gelatin sponges for 36 hours in charcoal-stripped serum media. Representative pieces of tumors were in parallel fixed in 4% formalin and subsequently immunohistochemistry for ER and PR protein was performed to assess the status of tumors for these receptors.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Hormone-treated explant was 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 |
Processed data file: Tumor N3.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) |
hari_singhal@dfci.harvard.edu
|
| 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. |
| GSE80365 |
Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer. [tumor samples RNA-seq] |
|
| Relations |
| BioSample |
SAMN04631338 |
| SRA |
SRX1688756 |
