|
| Status |
Public on Jul 07, 2011 |
| Title |
Sézary patient 1 (400k oligo array) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Peripheral blood mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
patient: 1
gender: female
disease state: Sézary syndrome
age: 76
time point of blood sample (mm/yy): 03/99
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA isolation was done according to standard protocols by performing proteinase K digestion and subsequent phenol/chloroform extraction or by using commercial DNA cleanup kits according to the manufacturer`s recommendations (QIAamp DNA Blood Mini Kit, QIAGEN, Hilden, Germany / PureLink Genomic DNA Mini Kit, Invitrogen, Karlsruhe, Germany). Samples with a low amount of DNA were amplified with the Sigma Whole Genome Amplification kit or illustra GenomiPhi V2 DNA Amplification kit (GE Healthcare), respectively.
|
| Label |
Cy3
|
| Label protocol |
see manufacturer website: http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90010_CGH_Enzymatic_Protocol_v6.2.pdf
|
| |
|
| Channel 2 |
| Source name |
lymphoblastoid cells
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
disease state: healthy control
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA isolation was done according to standard protocols by performing proteinase K digestion and subsequent phenol/chloroform extraction or by using commercial DNA cleanup kits according to the manufacturer`s recommendations (QIAamp DNA Blood Mini Kit, QIAGEN, Hilden, Germany / PureLink Genomic DNA Mini Kit, Invitrogen, Karlsruhe, Germany). Samples with a low amount of DNA were amplified with the Sigma Whole Genome Amplification kit or illustra GenomiPhi V2 DNA Amplification kit (GE Healthcare), respectively.
|
| Label |
Cy5
|
| Label protocol |
see manufacturer website: http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90010_CGH_Enzymatic_Protocol_v6.2.pdf
|
| |
|
| |
| Hybridization protocol |
see manufacturer website: http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90010_CGH_Enzymatic_Protocol_v6.2.pdf
|
| Scan protocol |
scanned on an Agilent DNA Microarray Scanner G2565BA, Scan resolution: 2µm, Scan region: 61 x 21.6 mm, Green PMT: 100%, Red PMT: 100%
|
| Description |
n/a
|
| Data processing |
TIFF image processing with Agilent Feature Extraction v10.5.1.1, CGH_105_Dec08 protocol
For visualization with CGHPRO (Chen et al. BMC Bioinformatics 2005) log2 ratios of the processed signals (from FE file) were subtracted: log2("gProcessedSignal")-log2("rProcessedSignal"). DNA copy number changes were defined by circular binary segmentation (Olshen et al. Biostatistics 2004) in combination with a log2 threshold of 0.2/-0.2.
|
| |
|
| Submission date |
Apr 14, 2010 |
| Last update date |
Nov 05, 2014 |
| 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 |
GPL19387 |
| Series (3) |
| 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 |
| GSE63013 |
The long isoform of RUNX3 acts as a tumor supressor in human T-cell lymphoma |
|
