|
| Status |
Public on Oct 07, 2013 |
| Title |
Prostate-Post-R2 |
| Sample type |
SRA |
| |
|
| Source name |
TRUSS-guided prostatic biopsy of clinically advanced/metastatic prostate cancer tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Prostate Tumour
time point: Post-Treatment
|
| Treatment protocol |
standard AAT consisting Luteinising hormone-releasing hormone (LHRH) agonists with anti-androgen “flare” protection. Repeat TRUSS biopsy was performed at ~22 weeks following initiation of AAT, specifically targeting tumour-rich areas
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from pre- and post-AAT samples using the RNeasy Mini Kit (QIAgen, 74104) according to manufacturer’s instructions. RNA quantity and quality was evaluated by spectrophotometry using the NanoDrop 2000 spectrophotometer (Thermo Scientific) and 2100 Bioanalyzer (Agilent) RNA electropherograms, with calculation of RNA integrity number (RIN) (35). Samples were included for RNA sequencing if RIN > 6 and total RNA > 500 ng
Samples were processed using the Illumina RNA-Seq protocol (Illumina) according to manufacturer’s instructions without poly(A) mRNA selection. The cDNA sample library was subsequently normalized using the Illumina DSN (Duplex-specific Nuclease) protocol according to manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Post treatment tumour sample from patient 2
|
| Data processing |
Basecalling was preformed using standard Illumina pipeline
Reads were mapped to the genome using TopHat v1.4.1, allow upto 2 mismatches and using a custom junctions library derived from Ensembl version 68
Reads falling in each gene model from Ensembl 68 were counted using HTSeq verion 0.5.3
Read counts were normalized using the TMM method via the edgeR bioconductor package and differentially expressed genes identified using a paired negative bionomial generalized linear model with the same package
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited table containing the read counts for each sample for each gene, and tab-delimited table of fitted expression changes with statistcal significance for each gene
|
| |
|
| Submission date |
Jun 28, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Ian Sudbery |
| E-mail(s) |
i.sudbery@sheffield.ac.uk
|
| Organization name |
University of Sheffield
|
| Department |
Molecular Biology and Biotechnology
|
| Lab |
Sudbery Lab for Computational Genomics
|
| Street address |
Firth Court, Western Bank
|
| City |
Sheffield |
| ZIP/Postal code |
S11 8HG |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE48403 |
The Wnt/β-catenin-signaling pathway is modulated by androgen ablation therapy for advanced clinical prostate cancer and contributes to androgen independent cell growth |
|
| Relations |
| SRA |
SRX316661 |
| BioSample |
SAMN02216946 |
