|
| Status |
Public on Mar 01, 2018 |
| Title |
PatientD_2005_2N |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Prostate
|
| Organism |
Homo sapiens |
| Characteristics |
amplification: phi29
ploidy: 2N
|
| Growth protocol |
Tumor samples from patients with prostate carcinoma were flash-frozen and maintaned at -80 degrees C until processed for flow sorting
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
25-100 mg of tumor was thawed then minced in the presence of NST and DAPI. Each sample was then mechanically sheared then filtered through a 30 micron mesh filter prior to sorting. All sorting was done with an Influx Flow Cytometer equiped with a UV laser. DNA was extracted from each sorted fraction using Qiagen DNA micro kits. All phi29 amplifications were done with a 100ng aliquot of either sample or reference genomic DNA using the GenomiPhi kit (G.E Health Care)
|
| Label |
Cy5
|
| Label protocol |
A 1 microgram aliquot of each sample and reference DNA was digested with DNAse 1 then labeled with a fluorescent nucleotide (Cy5 for tumor and Cy3 for normal reference) using the BioPrime labeling kit (Invitrogen)according to manufacturer's protocol.
|
| |
|
| Channel 2 |
| Source name |
pooled 46, XX DNA (Promega, Madison, WI)
|
| Organism |
Homo sapiens |
| Characteristics |
amplification: phi29
sample type: reference
|
| Growth protocol |
Tumor samples from patients with prostate carcinoma were flash-frozen and maintaned at -80 degrees C until processed for flow sorting
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
25-100 mg of tumor was thawed then minced in the presence of NST and DAPI. Each sample was then mechanically sheared then filtered through a 30 micron mesh filter prior to sorting. All sorting was done with an Influx Flow Cytometer equiped with a UV laser. DNA was extracted from each sorted fraction using Qiagen DNA micro kits. All phi29 amplifications were done with a 100ng aliquot of either sample or reference genomic DNA using the GenomiPhi kit (G.E Health Care)
|
| Label |
Cy3
|
| Label protocol |
A 1 microgram aliquot of each sample and reference DNA was digested with DNAse 1 then labeled with a fluorescent nucleotide (Cy5 for tumor and Cy3 for normal reference) using the BioPrime labeling kit (Invitrogen)according to manufacturer's protocol.
|
| |
|
| |
| Hybridization protocol |
Labeled DNAs were hybridized in an ozone free environment in a rotisserie oven at 20 rpm for 40 hours then washed according to array supplier's (Agilent)protocol
|
| Scan protocol |
All microarray slides were scanned using an Agilent G2505C DNA scanner and default settings for CGH.
|
| Data processing |
Data was extracted from the TIFF files using Agilent FE 10.5. The data quality was assessed using the QC Report output in F.E. 10.5. All arrays that passed the experimental Q.C. were then analysed using the Limma package in the R environment. With minimum background correction and printtiploess normalization.
|
| |
|
| Submission date |
Dec 18, 2017 |
| Last update date |
Mar 01, 2018 |
| Contact name |
Joël Roman Federer-Gsponer |
| Organization name |
University Hospital Basel
|
| Department |
Department of Pathology
|
| Street address |
Tangentenweg 34
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL9777 |
| Series (1) |
| GSE108203 |
Tumor evolution in the context of castration resistance in prostate cancer |
|
