|
| Status |
Public on Dec 30, 2016 |
| Title |
WT day46 rep1 SNP |
| Sample type |
genomic |
| |
|
| Source name |
tumor cells
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6N
genotype/variation: wild type
cell type: tumor cells
time point: day 46
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genome-wide copy number profiles of two wt samples (day 23 and day 46), two RAG1-/- samples (day 13 and day 23), three aPD-L1 and three IgG2b samples, MC38 and skin germline DNA were obtained using the Affymetrix Mouse Diversity Array. The genotyping analyses were carried out at Eurofins Genomics (Ebersberg, Germany) using Affymetrix Mouse Diversity Array.
|
| Label |
biotin
|
| Label protocol |
standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
standard Affymetrix protocol
|
| Scan protocol |
standard Affymetrix protocol
|
| Description |
Affymetrix Mouse Diversity Array
|
| Data processing |
The SNP arrays were processed, quantile-normalized, and median-polished using the Aroma Affymetrix CRMAv2 algorithm. Copy number alteration (CNA) for each probe were computed as log2-ratios between the probe signal intensities of each sample and the reference skin sample and then those ratios were segmented using the circular binary segmentation algorithm implemented in the R package DNAcopy
*_cna.txt: Segmented CNA - output from DNAcopy
|
| |
|
| Submission date |
Dec 30, 2016 |
| Last update date |
Dec 30, 2016 |
| Contact name |
Mirjana Efremova |
| E-mail(s) |
mirjana.efremova@i-med.ac.at
|
| Organization name |
Medical University of Innsbruck
|
| Street address |
Innrain 80-82
|
| City |
Innsbruck |
| ZIP/Postal code |
6020 |
| Country |
Austria |
| |
|
| Platform ID |
GPL13147 |
| Series (2) |
| GSE93016 |
Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinoma [SNP] |
| GSE93018 |
Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinoma |
|
