|
| Status |
Public on Jun 19, 2008 |
| Title |
Nodal DLBCL 12N |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Nodal DLBCL
|
| Organism |
Homo sapiens |
| Characteristics |
Tissue: Nodal diffuse large B cell lymphoma, Sample origin: Whole frozen tissue sections, Sample type: DNA, Gender: Male
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using high salt after overnight SDS/proteinase K digestion.
|
| Label |
Cy3
|
| Label protocol |
450 ng genomic DNA was labeled using Cy3- or Cy5-dCTP in an overnight random prime labeling reaction (BioPrime Random Prime labelling Kit, Invitrogen). Labeled test and reference samples were pooled and precipitated in the presence of Cot1 DNA.
|
| |
|
| Channel 2 |
| Source name |
Pooled reference DNA
|
| Organism |
Homo sapiens |
| Characteristics |
commercially available female DNAs (Promega, Leiden, the Netherlands) that represent DNA pools derived from at least seven individuals
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using high salt after overnight SDS/proteinase K digestion.
|
| Label |
Cy5
|
| Label protocol |
450 ng genomic DNA was labeled using Cy3- or Cy5-dCTP in an overnight random prime labeling reaction (BioPrime Random Prime labelling Kit, Invitrogen). Labeled test and reference samples were pooled and precipitated in the presence of Cot1 DNA.
|
| |
|
| |
| Hybridization protocol |
DNA pellet was dissolved in hybridisation mixture. Sample was hybridized for 20 hours followed by post-hybridisation washes and drying of slides by using an automated hybridisation station (Tecan Benelux BVBA).
|
| Scan protocol |
Slides were scanned on a GenePix 4100A scanner (Axon Instruments, Westburg BV).
|
| Description |
Gender mismatch hybridisation
|
| Data processing |
Scanned images were processed using GenePix Pro 4.1 software. Pixel intensities for each feature were integrated and median values were determined, and the local background was calculated. For each spot the intensities were corrected (pixel median values) by subtracting the local background (pixel median values) for both wavelengths. The median of the ratios of all spots was calculated and used to normalize all data points. As quality control, spots outside the 20% confidence interval of the average of the replicate were excluded. Only those targets presenting at least two spots within 20% confidence interval of their average were used. For each feature (3 spots), the log2 value of the average of the normalized ratios of the three spots was calculated.
|
| |
|
| Submission date |
Feb 14, 2008 |
| Last update date |
Jun 19, 2008 |
| Contact name |
Marije Booman |
| E-mail(s) |
[email protected]
|
| Organization name |
University Medical Center Groningen
|
| Department |
Pathology
|
| Street address |
P.O. Box 30001
|
| City |
Groningen |
| ZIP/Postal code |
9700 RB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL4012 |
| Series (1) |
| GSE10524 |
Genomic alterations and gene expression in primary diffuse large B cell lymphomas of immune privileged sites |
|
