|
| Status |
Public on Apr 06, 2017 |
| Title |
CLL022-postRS-RT |
| Sample type |
genomic |
| |
|
| Source name |
CLL022_lymph node
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: ibrutinib-relapsed CLL patients
subject id: CLL022
disease stage: LN-richter transformation
tissue: lymph node
|
| Treatment protocol |
None
|
| Growth protocol |
None
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from fresh tissue, peripheral blood or bone marrow at defined time points during treatment and/or disease course using the Qiagen DNA Blood Mini Kit or QIAmp DNA for FFPE tissue kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, Qubit fluorometer or PicoGreen and agarose gel electrophoresis.
|
| Label |
Biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Data processing |
The array image was acquired using Affymetrix Molecular Diagnostic Software (AMDS version 1.1). Copy number values for individual probes is extracted and converted to an intensity data (CEL) file by and subsequently converted graphical, tabular and segmental data files (CYCHP for CytoScan, OSCHP for OncoScan) using Affymetrix Chromosome Analysis Suite (ChAS 3.0) software. Estimation of ploidy and aberrant call percentage in OSCHP files is calculated using the TuScan algorithm.
|
| |
|
| Submission date |
Apr 05, 2017 |
| Last update date |
Apr 06, 2017 |
| Contact name |
Carrie A Fitzpatrick |
| Organization name |
University of Chicago
|
| Street address |
5841 S Maryland Ave
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL21558 |
| Series (1) |
| GSE97436 |
Affymetrix SNP array data for chronic lymphoblastic leukemia samples |
|
