|
| Status |
Public on May 22, 2015 |
| Title |
T47D_E2+R5020_3hr_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
T47D_E2+R5020_3hr
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: T47D
cell type: ER+ breast cancer cell line
treated with: E2+R5020_3hr
|
| Treatment protocol |
Cells were treated with progesterone (100nM) or R5020 (10nM) for 3hr and RNA extracted
|
| Growth protocol |
Cells grown in DMEM, supplemented with 10% FBS
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA (miRNeasy kit, Qiagen) from the flow sorted cells was used to prepare libraries using the TruSeq RNA sample preparation kit (Illumina).
as per instructions from the TruSeq RNA sample preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA-seq from T47D cells treated with E2+R5020_3hr (Replicate 1)
|
| Data processing |
Single-end 40 bp reads generated on Illumina HiSeq were aligned to the human genome version GRCh37.64 using TopHat v2.0.4 (Trapnell et al., 2009). Read counts were obtained using HTSeq-count v0.5.3p9 (Anders et al., 2014).
Read counts were normalised and tested for differential gene expression using the DESeq5 workflow. Multiple testing correction was applied using the Benjamini-Hochberg method. Genes were selected as differentially expressed such that FDR <0.01.
Genome_build: GRCh37.64
Supplementary_files_format_and_content: HTSeq-count gene counts
|
| |
|
| Submission date |
Apr 28, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Chandra Chilamakuri |
| E-mail(s) |
datasubmissions@cruk.cam.ac.uk
|
| Organization name |
Cancer Research UK Cambridge Institute
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE68358 |
RNA-seq in two ER+ breast cancer cell lines with and without progestins |
| GSE68359 |
Progesterone receptor directs a distinct estrogen receptor-alpha chromatin binding profile in breast cancer to elicit good clinical outcome |
|
| Relations |
| BioSample |
SAMN03570779 |
| SRA |
SRX1012813 |
