|
| Status |
Public on Jan 18, 2021 |
| Title |
ZR-75-1 xenograft Vehicle 1 |
| Sample type |
SRA |
| |
|
| Source name |
ZR-75-1 xenograft Vehicle tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: ZR-75-1 cell line xenograft tumor
treatment: Vehicle
time point: Short-term (5 days treatment)
replicate: 1
|
| Treatment protocol |
Mice were randomly assigned to treatment groups and treated for 5 days with either a vehicle, enzalutamide (Enza), DHT, or enobosarm (SARM). Enza (20 mg/kg/day) and SARM (10 mg/kg/day) was dissolved in 10% Tween 80 and delivered daily by oral gavage. DHT pellets were surgically implanted subcutaneously. After 5 days, tumors were excised and snap-frozen.
|
| Growth protocol |
Athymic nude mice were subcutaneously implanted with an E2 pellet and injected with 5x10^6 (20 µL) ZR-75-1 cells into the fourth inguinal mammary fat pad. Tumors were allowed to grow until reaching ~200 mm^3 size before beginning treatment.
|
| 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 and sequenced on the Illumina HiSeq 2500 (v4.0) with 125 bp paired-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Xeno_Veh_Tum1_015
processed data file:
Xeno_genes.tpm.filtered.txt
Xeno_genes.fpkm.txt
Xeno_genes.fpkm.filtered.txt
Xeno_genes.counts.txt
Xeno_genes.counts.filtered.txt
|
| Data processing |
Basecalls performed using Illumina bcl2fastq.
Fastq files were quality checked (FastQC v0.11.4; fastq-screen v0.5.2). Sequence adapters were trimmed using cutadapt v1.9.1 (Martin, 2011).
Host reads were removed with Xenome v1.0.1 (Conway et al., 2012) and human sequences were aligned to hg38 using STAR v2.4.2a (Dobin et al., 2013).
Sequences identified as originating from the graft were then aligned to the hg38 reference genome using STAR, version 2.4.2a (Dobin et al., 2013).
Gene feature counting was performed with RSEM v1.2.21 (Li & Dewey, 2011).
Transcripts with expression counts of 0 across all samples were removed and then normalized using TMM (Robinson & Oshlack, 2010).
Transcripts with zero expression counts across all samples were removed. TMM normalized counts (Robinson & Oshlack, 2010) were log transformed using voom (Law et al., 2014) and differential expression was performed with limma (Smyth, 2004).
Moderated F-statistics were calculated and genes that were significantly differentially regulated (with a Benjamini-Hochberg adjusted p-value (BH) <0.05) between the treatment groups were identified.
Genome_build: hg38
Supplementary_files_format_and_content: Differential expression of vehicle, enzalutamide, DHT, and enobosarm-treated ZR-75-1 tumors.
|
| |
|
| 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) |
| GSE123766 |
The Androgen Receptor is a Tumor Suppressor in Estrogen Receptor Positive Breast Cancer [ZR-75-1 xenograft RNA-seq] |
| GSE123770 |
The Androgen Receptor is a Tumor Suppressor in Estrogen Receptor Positive Breast Cancer |
|
| Relations |
| BioSample |
SAMN10588052 |
| SRA |
SRX5128113 |
