|
| Status |
Public on May 10, 2018 |
| Title |
LuCaP 170 2 organoids G8 2 |
| Sample type |
genomic |
| |
|
| Source name |
LuCaP 170 2 organoids G8
|
| Organism |
Homo sapiens |
| Characteristics |
subject id: LuCaP 170.2
gender: male
tissue: PDX-derived organoid
generation: G8
replicate: 2
|
| Treatment protocol |
Organoids were passaged.
|
| Growth protocol |
LuCaP tumors were grown in mice or as organoids.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from fresh frozen PDX tissue and from fresh organoids, using a Qiagen AllPrep DNA/RNA Mini Kit.
|
| Label |
Allele-specific single base extension of the primer incorporates a biotin nucleotide or a dinitrophenyl labeled nucleotide. C and G nucleotides are biotin labeled; A and T nucleotides are dinitrophenyl labeled.
|
| Label protocol |
Samples were labeled using Infinium probe designs.
|
| |
|
| Hybridization protocol |
SDNA from each sample was quality checked using an Agilent TapeStation 2200 and PicoGreen Assay, and an aliquot of 200 ng of DNA was fragmented and prepared into libraries for hybridization to Illumina OmniExpress BeadChip Arrays at the National Cancer Institute, Cancer Genomics Research Laboratory.
|
| Scan protocol |
Samples were scanned using an iScan system.
|
| Description |
200627820019_R08C02
LuCaP170.2-G8-Rep2
|
| Data processing |
Data was clustered against a panel of normal provided by Illumina using GenomeStudio (Illumina) and exported for analyses in Nexus Copy Number version 8 (BioDiscovery) used for calling somatic copy number alterations.
the 'SomaticCopyNumber.seg' contains the log2 copy number values generated from probe medians derived by Nexus Copy Number, for each segment of the genome.
|
| |
|
| Submission date |
Apr 26, 2018 |
| Last update date |
May 10, 2018 |
| Contact name |
Adam Sowalsky |
| Organization name |
National Cancer Institute
|
| Department |
LGCP
|
| Lab |
Sowalsky Lab
|
| Street address |
37 Convent Drive Building 37 Room 1062B
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL22678 |
| Series (2) |
| GSE113709 |
Establishment and characterization of prostate cancer organoids [array] |
| GSE113743 |
Establishment and characterization of prostate cancer organoids |
|
