|
| Status |
Public on Mar 26, 2018 |
| Title |
HumanOmni2.5 CAF2 |
| Sample type |
genomic |
| |
|
| Source name |
CAF
|
| Organism |
Homo sapiens |
| Characteristics |
patient: 2
gender: Male
tissue: Prostate
cell type: Cancer Associated Fibroblast
|
| Treatment protocol |
Cells were cultured in standard media to approximately 80% confluency before being trypsinised, resuspended in media and then centrifuged to create cell pellets. Cells were stored at -80°C until DNA extraction.
|
| Growth protocol |
Prostate tissue was chopped into small pieces, approximately 2 mm3, and digested overnight at 37°C in RPMI containing 10% fetal calf serum (FCS), 25 mM HEPES, 100 U/mL penicillin, 100 mg/mL streptomycin, 0.5 mg/mL fungizone, 100 mg/mL gentamicin, 225 U/mL Collagenase Type I and 125 U/mL Hyaluronidase Type II (Sigma Aldrich) as previously described [PMID: 23558784]. Cell suspensions were seeded in RPMI containing 5% FCS, penicillin/streptomycin, 1 nM testosterone (Sigma Aldrich) and 10 ng/mL bFGF (Millipore), a medium that selects for fibroblasts compared to other prostatic cell types. Cells were grown at 37°C in a humidified incubator with 5% O2 and 5% CO2. The first passage of cells typically reached confluency within 2 weeks. The cells were used between passages 2-6.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from CAF and NPF samples using the DNeasy kit (Qiagen) with on-column RNase A digestion. Eluates were precipitated with 0.1 volume sodium acetate and 2.5 volumes ethanol and then resuspended in nuclease-free water. DNA was quantified using a NanoDrop 2000. 200ng of DNA was quantified using the Illumina HumanOmni2.5-8 Beadchip (Illumina, CA, USA)
|
| Label |
biotin
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Standard Illumina Protocol
|
| Scan protocol |
Standard Illumina Protocol
|
| Description |
CAF2
|
| Data processing |
Copy numbers were estimated using circular binary segmentation (CBS) [PMID: 15475419] to translate intensity measurements into regions of equal copy number. The raw array data was processed using crlmm (v1.25.1) [PMID: 19661241] for background correction and normalization, accounting for batch effects.The resulting log R ratios were then smoothed to remove outliers prior to segmentation (R package DNAcopy). All analyses were carried out in R3.1.2 (www.r-project.org).
Tab delimited text files - LogR ratio (LRR), B allele frequency (BAF) and genotype calls (1=AA, 2=AB, 3=BB)
|
| |
|
| Submission date |
Aug 15, 2016 |
| Last update date |
Mar 26, 2018 |
| Contact name |
Ruth Pidsley |
| E-mail(s) |
r.pidsley@garvan.org.au
|
| Organization name |
Garvan Institute of Medical Research
|
| Street address |
384 Victoria Street
|
| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL16104 |
| Series (2) |
| GSE85605 |
Cancer Associated Fibroblasts are defined by a core set of epigenome changes that contribute to the tumor phenotype [Illumina_Omini 2.5-8_SNP] |
| GSE86260 |
Cancer Associated Fibroblasts are defined by a core set of epigenome changes that contribute to the tumor phenotype |
|
