|
| Status |
Public on Jan 18, 2021 |
| Title |
TH-107 ED |
| Sample type |
SRA |
| |
|
| Source name |
Normal breast_E2+DHT
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: 107
tissue type: Normal breast
treatment: E2+DHT
|
| Treatment protocol |
PDEs were treated for 24h with either 10nM E2 or 10nM E2 + 10nM DHT.
|
| Growth protocol |
Patient tissue specimens were cut into small pieces, randomly allocated to a gelatin sponge (3-4 per sponge), pre-soaked in culture media, and incubated at 37°C with 5% CO2 for ~ 36 hours as 'patient-derived explants' (PDEs).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen RNeasy kit, according to the manufacturer's instructions.
Libraries were generated using the TruSeq Stranded Mrna Library Prep Kit
RNA-Seq; Illumina HiSeq 2500 40bp single-end reads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
TH-107 ED
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx
|
| Data processing |
Basecalls performed using Illumina software
hg19 alignment was performed using CLC Genomics Workbench 11 (QIAGEN) using the following mapping parameters: Mismatch cost 2; Insertion cost 3; Deletion cost 3; Length fraction 0.8; Similarity fraction 0.8.
Treatment comparisons were performed on samples individually due to tissue heterogeneity. Genes common between both Kahl's Z-test (FDR <0.01; Kal et al., 1999) and Baggerley's test (FDR <0.01; Baggerly et al., 2003) were determined to be significantly differentially regulated.
Expression was measured based on the total counts of mapped short reads and normalised based on RPKM (CLC Genomics Workbench).
Genome_build: hg19
Supplementary_files_format_and_content: Processed data presented as RPKM
|
| |
|
| Submission date |
Dec 13, 2018 |
| Last update date |
Jan 18, 2021 |
| Contact name |
Luke Selth |
| E-mail(s) |
luke.selth@flinders.edu.au
|
| Organization name |
Flinders University
|
| Department |
College of Medicine and Public Health
|
| Street address |
Flinders Drive
|
| City |
Bedford Park |
| State/province |
SA |
| ZIP/Postal code |
5042 |
| Country |
Australia |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE123762 |
The Androgen Receptor is a Tumor Suppressor in Estrogen Receptor Positive Breast Cancer [Normal and tumor patient-derived explant RNA-seq] |
| GSE123770 |
The Androgen Receptor is a Tumor Suppressor in Estrogen Receptor Positive Breast Cancer |
|
| Relations |
| BioSample |
SAMN10587993 |
| SRA |
SRX5133385 |
