|
| Status |
Public on Sep 12, 2016 |
| Title |
PrEC Rep1 |
| Sample type |
genomic |
| |
|
| Source name |
PrEC cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary prostate epithelial cells (PrEC)
|
| Growth protocol |
LNCaP prostate cancer cells were cultured as described in PMID 11850822. Normal prostate epithelial cells (PrEC) were cultured according to the manufacturer’s instructions in prostate epithelial growth medium (PrEGM, catalogue no. CC-3166; Cambrex Bio Science) as described in PMID 20173741. Patient-matched cancer associated fibroblasts (CAFs) and non-malignant tissue associated fibroblasts (NAFs) (n=3 pairs) were isolated and validated as described in PMID 23558784
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA for LNCaP and PrEC cell lines was extracted using QIAamp DNA Mini and Blood Mini kit following the manufacturer’s protocol for cultured cells (Qiagen). Genomic DNA was extracted from the CAF and NAF samples using the DNeasy kit (Qiagen) with on-column RNase A digestion. Genomic DNA was extracted from the Guthrie cards using GenSolve technology (IntegenX) followed by purification using the QIAamp DNA micro kit (Qiagen) and an additional ethanol precipitation step.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol
|
| Scan protocol |
Standard Illumina Protocol
|
| Description |
primary cell culture of prostate epithelial cells
|
| Data processing |
Raw IDAT files were processed with Illumina’s GenomeStudio software V2011.1 and background normalized using negative control probes to generate methylation β-values which were used for all downstream analyses.
|
| |
|
| Submission date |
Sep 12, 2016 |
| Last update date |
Sep 12, 2016 |
| Contact name |
Ruth Pidsley |
| E-mail(s) |
[email protected]
|
| 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 |
GPL21145 |
| Series (2) |
| GSE86831 |
Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling [MethylationEPIC] |
| GSE86833 |
Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling |
|
