|
| Status |
Public on Dec 31, 2017 |
| Title |
T47D xenografts_RNA-seq_EC313+ICI |
| Sample type |
SRA |
| |
|
| Source name |
T47D Xenografts
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: T47D Xenografts
er/pr status: ER+/PR+
drug treatment: EC313+ICI
hormone exposure time: 3 weeks
|
| Treatment protocol |
PR agonists (progesterone, MPA and R5020), PR-agonistic antagonist EC313, PR antagonist CDB4453 and SERMs (tamoxifen, raloxifene, bazedoxifene and fulvestrant), mice were injected intra-peritoneal for three weeks with 10 mg/kg/day of the respective drugs. Five injections per week were administered. Mice in the CDB4124 experiment arm (Vehicle, CDB4124, Tamoxifen or CDB4124+Tamoxifen) were administered using 25 mg drug pellets. At the end of the duration of the experiment, mice were sacrificed; tumors were excised, weighed, fixed and snap-frozen for later analyses. RNA-seq was performed on these harvested xenografts. (Xenograft experiments).
|
| Growth protocol |
Xenografts: Nude mice harboring ER+/PR+ T47D xenografts were treated with various drug combinations for at least 3 weeks. Drugs were either admnistered in the form of intra-peritoneal injections or as 25 mg 90 day release drug pellets (Innovative Research of America).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Frozen xenograft tumors were finely grinded using cold hammer and a pestle. The pestle was placed over dry ice to maintain it at low temperatures. The ground tumor was suspended in ice-cold PBS and dounce homogenized and subsequently washed twice with ice-cold PBS.
The cell pellets obtained from and washed xenografts were processed similar to the pellets obtained from in-vitro experiments (RNA-seq 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 NextSeq 500 |
| |
|
| Description |
T47D_Xenografts_readcounts
|
| 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: Matrix containing normalized readcounts from each of the samples has been provided
|
| |
|
| Submission date |
Jun 01, 2017 |
| 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 |
GPL18573 |
| Series (2) |
| GSE80619 |
T47D xenografts treated with various combinations of ER- and PR-targeting therapies |
| GSE80620 |
Progesterone Receptor Isoforms, Agonists and Antagonists Differentially Reprogram Estrogen Signaling. |
|
| Relations |
| BioSample |
SAMN07189698 |
| SRA |
SRX2880449 |
