|
| Status |
Public on Dec 01, 2015 |
| Title |
Normal_DNA_16712 |
| Sample type |
genomic |
| |
|
| Source name |
genomic DNA extracted from saliva of patient 10864
|
| Organism |
Homo sapiens |
| Characteristics |
sample id: N_16712
disease state: NMZL
individual: patient 10864
tissue: tumor free bone marrow
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Not applicable
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified by cell lysis followed by digestion with proteinase K, “salting out” extraction, and ethanol precipitation. DNA was quantified by the Quant-iT PicoGreen reagent (Invitrogen). All DNA samples were verified for integrity by 0.8% agarose gel electrophoresis.
|
| Label |
Biotin
|
| Label protocol |
Sample DNA was digested by restriction enzymes NspI, adaptors were ligated to the diagested DNA to perform a PCR amplification. Amplified DNA was labeled and further fragmented using Affymetrix Cytoscan HD array kit and reagent kit bundle, (Affymetrix, Santa Clara, CA,US) to obtain biotin labeled DNA, as per manufacturer’s instruction.
|
| |
|
| Hybridization protocol |
Sample DNA was digested by restriction enzymes NspI, adaptors were ligated to the diagested DNA to perform a PCR amplification. Amplified DNA was labeled and further fragmented using Affymetrix Cytoscan HD array kit and reagent kit bundle, (Affymetrix, Santa Clara, CA,US) to obtain biotin labeled DNA, as per manufacturer’s instruction.
|
| Scan protocol |
The Arrays were washed using affymetrix fluidics stations FS450 and scanned using the Gene Chip Scanner 3000.
|
| Description |
19N
Hybridized to Cytoscan HD array Affymetrix
|
| Data processing |
Raw data passed quality control were further analyzed by Affymetrix® Chromosome Analysis Suite (Affymetrix, Santa Clara, CA, US). CEL files were generated from the scanned array image files by the Affymetrix GeneChip Command Console Software and were imported into the Affymetrix Chromosome Analysis Suite v1.2.0 Software. Copy number and genotyping data files (cyhd.cychp and cyhd.txt files) were generated using ChAS (cyhd.cychp files are displayed in the Sample data table below). The identification of regions of abnormal copy number was performed both by ChAs and by a pipeline that embed the circular binary segmentation as detailed in previously published papers: normalization was performed using the reference normalization algorithm developed at St Jude and described in Mullighan et al Nature 2007;446:758. The data matrix contains the normalized expression values produced by that algorithm (NMZL_cnmz.txt: matrix of the 35 NMZL and 23 paired normal DNAs). All the CNAs were visually inspected by dChip sopftware (https://sites.google.com/site/dchipsoft/).
|
| |
|
| Submission date |
Apr 20, 2015 |
| Last update date |
Dec 01, 2015 |
| Contact name |
Valeria Spina |
| Organization name |
Amedeo Avogadro University of Eastern Piedmont
|
| Department |
Translational Medicine
|
| Lab |
Hematology
|
| Street address |
Solaroli, 17
|
| City |
Novara |
| State/province |
NO |
| ZIP/Postal code |
28100 |
| Country |
Italy |
| |
|
| Platform ID |
GPL16131 |
| Series (1) |
| GSE68078 |
Cytoscan HD arrays data for Nodal marginal zone lymphoma (NMZL) |
|
