|
| Status |
Public on Jan 24, 2018 |
| Title |
PPAB_25_4b-PPT_244k |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Primary pancreatic cancer cell culture
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: mixed (C57Bl/6;129S6/SvEv)
genotype/variation: PK-PB
originating tissue: pancreatic cancer
|
| Treatment protocol |
No treatment was applied.
|
| Growth protocol |
For all primary culture experiments, culturing medium (DMEM supplemented with 10% FCS and 1x P/S) and cultures with less than 10 passages were used.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA from murine primary cell culture pellets was isolated using the DNeasy Blood & Tissue Kit (Qiagen) according to manufacturer’s instructions.
|
| Label |
Cy5
|
| Label protocol |
250ng of genomic DNA were fluorescence labelled (Cy3 sample and Cy5 reference) by random primed labelling using the Enzo Oligo Array CGH Labelling kit according to the manufacturer's protocol. The labelling activity was determined using a NanoDrop spectrophotometer.
|
| |
|
| Channel 2 |
| Source name |
Corresponding tail
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: mixed (C57Bl/6;129S6/SvEv)
genotype/variation: PK-PB
originating tissue: tail
|
| Treatment protocol |
No treatment was applied.
|
| Growth protocol |
For all primary culture experiments, culturing medium (DMEM supplemented with 10% FCS and 1x P/S) and cultures with less than 10 passages were used.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA from murine primary cell culture pellets was isolated using the DNeasy Blood & Tissue Kit (Qiagen) according to manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
250ng of genomic DNA were fluorescence labelled (Cy3 sample and Cy5 reference) by random primed labelling using the Enzo Oligo Array CGH Labelling kit according to the manufacturer's protocol. The labelling activity was determined using a NanoDrop spectrophotometer.
|
| |
|
| |
| Hybridization protocol |
The labelled DNA was hybridised onto the array slides in a 24h incubation at 65°C according to the manufacturer's (Agilent) protocol.
|
| Scan protocol |
The slides were washed and scanned and the data extracted as tab-delimited text files according to the manufacturer's protocol.
|
| Description |
PK-PB mouse
|
| Data processing |
Agilent Genomic Workbench software v7.0.4.0 was used for aCGH data preprocessing. Legacy centralization option was used for re-centralization of raw log ratios to the most common ploidy state. ADM-2 algorithm was applied for aberration calling. Normalized and curated data was imported into R.
|
| |
|
| Submission date |
Nov 28, 2017 |
| Last update date |
Jan 25, 2018 |
| Contact name |
Roland Rad |
| E-mail(s) |
[email protected]
|
| Organization name |
Center for Translational Cancer Research (TranslaTUM)
|
| Lab |
Experimental cancer genetics and translational genomics
|
| Street address |
Ismaninger Str. 22
|
| City |
Munich |
| State/province |
Bavaria |
| ZIP/Postal code |
81675 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15076 |
| Series (2) |
| GSE107454 |
Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes [aCGH] |
| GSE107458 |
Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes |
|
