|
| Status |
Public on Jul 07, 2011 |
| Title |
Sézary patient 3 (BAC array) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
DNA isolated from living peripheral blood mononuclear cells (PBMC) of patient
|
| Organism |
Homo sapiens |
| Characteristics |
patient: 3
gender: female
disease state: Sézary syndrome
age: 95
time point of blood sample (mm/yy): 08/99
|
| Treatment protocol |
Whole genome amplification by GenomePlex (Sigma)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Living PBMCs were digested with proteinase K followed by phenol/chloroform/isopropanol DNA purification.
|
| Label |
Alexa Fluor 3
|
| Label protocol |
DNA was labelled by random priming according Invitrogens recommendation (Invitrogen BioPrime® Total Genomic Labeling System). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics).
|
| |
|
| Channel 2 |
| Source name |
DNA pool isolated from living peripheral blood mononuclear cells (PBMC) of healthy donors
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
disease state: healthy control
|
| Treatment protocol |
Whole genome amplification by GenomePlex (Sigma)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA of MeOH/Hac fixated PBMCs were isolated with phenol/chloroform/ isopropanol.
|
| Label |
Alexa Fluor 5
|
| Label protocol |
DNA was labelled by random priming according Invitrogens recommendation (Invitrogen BioPrime® Total Genomic Labeling System). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics).
|
| |
|
| |
| Hybridization protocol |
Hybridization was done overnight at 42°C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics).
|
| Scan protocol |
Slides were scanned at 10 µm resolution using an Agilent scanner (G2565BA). PMT settings: 100/100
|
| Description |
Array CGH analysis of a female patient with Sézary syndrome.
|
| Data processing |
TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005). Background intensities were not subtracted. Signal intensities were normalized by subgridd LOWESS. Aberrations were defined by Circular Binary Segmentation in combination with log2 ratio threshold of 0.2 and -0.2, respectively.
|
| |
|
| Submission date |
Nov 12, 2009 |
| Last update date |
Jul 07, 2011 |
| Contact name |
Reinhard Ullmann |
| E-mail(s) |
ullmann@molgen.mpg.de
|
| Phone |
00493084131251
|
| Organization name |
MPIMG
|
| Department |
Human Molecular Genetics
|
| Lab |
Molecular Cytogenetics
|
| Street address |
Ihnestr.73
|
| City |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
| |
|
| Platform ID |
GPL5114 |
| Series (2) |
| GSE19000 |
Comparative genomic hybridization of 20 patients with Sézary syndrome |
| GSE21731 |
Genomic loss of the putative tumor suppressor gene E2A promotes cutaneous T-cell lymphoma in human |
|
