|
| Status |
Public on Jun 01, 2016 |
| Title |
Non-relapsing_DLBCL_primary (case40) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
FFPE tissue biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Diffuse large B cell lymphoma (DLBCL)
specimen: Non-relapsing DLBCL primary
|
| Treatment protocol |
na
|
| Growth protocol |
na
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
H&E- and CD20-stained sections of FFPE blocks or fresh-frozen tissue were reviewed to evaluate tumor content. Only tissues with >70% tumor content were used. Depending on the distribution of tumor cells, 25µm-thick sections were cut or punches were taken from the tumor-rich tissue areas. Prior to overnight Proteinase K digestion, paraffin sections were deparaffinized and rehydrated by serial xylene and ethanol washes, respectively. Genomic DNA (gDNA) was extracted by automation using Maxwell® 16 FFPE plus LEV DNA Purification Kit. gDNA from samples with extremely scarce tumor material was isolated by the phenol-chloroform extraction as described previously22. Yields were quantified by the Qubit assay.
|
| Label |
cy5
|
| Label protocol |
A 100-500 nanogram aliquot of each sample and reference DNA was heat digested then labeled with a fluorescent nucleotide (Cy5 for tumor and Cy3 for normal reference) using the BioPrime labeling kit (Invitrogen)according to manufacturer's protocol.
|
| |
|
| Channel 2 |
| Source name |
Reference pooled 46XX
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pooled normal (46,XX) reference (Promega)
|
| Treatment protocol |
na
|
| Growth protocol |
na
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
H&E- and CD20-stained sections of FFPE blocks or fresh-frozen tissue were reviewed to evaluate tumor content. Only tissues with >70% tumor content were used. Depending on the distribution of tumor cells, 25µm-thick sections were cut or punches were taken from the tumor-rich tissue areas. Prior to overnight Proteinase K digestion, paraffin sections were deparaffinized and rehydrated by serial xylene and ethanol washes, respectively. Genomic DNA (gDNA) was extracted by automation using Maxwell® 16 FFPE plus LEV DNA Purification Kit. gDNA from samples with extremely scarce tumor material was isolated by the phenol-chloroform extraction as described previously22. Yields were quantified by the Qubit assay.
|
| Label |
cy3
|
| Label protocol |
A 100-500 nanogram aliquot of each sample and reference DNA was heat digested then labeled with a fluorescent nucleotide (Cy5 for tumor and Cy3 for normal reference) using the BioPrime labeling kit (Invitrogen)according to manufacturer's protocol.
|
| |
|
| |
| Hybridization protocol |
Labeled DNAs were hybridized in an ozone free environment in a rotisserie oven at 25 rpm for at least 24 hours then washed according to array supplier's (Agilent)protocol
|
| Scan protocol |
All arrays were scanned using an Agilent 2565C Scanner and default settings for CGH.
|
| Description |
BIP_case40_primary
|
| Data processing |
Data was extracted from the TIFF files using Agilent FE 10.5. The data quality was assessed using the QC Report output in F.E. 10.5. All arrays that passed the experimental Q.C. were then visulaized and analyzed using Agilent Genomic Workbench v7.0 and the ADM2 algorithm.
|
| |
|
| Submission date |
May 06, 2016 |
| Last update date |
Jun 01, 2016 |
| Contact name |
Darius Juskevicius |
| E-mail(s) |
JuskeviciusD@uhbs.ch
|
| Organization name |
Institute of Pathology
|
| Department |
Molecuar Pathology
|
| Street address |
Schoenbeinstr. 40
|
| City |
Basel |
| ZIP/Postal code |
4031 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL10123 |
| Series (1) |
| GSE65720 |
Clonal relationship of relapsing diffuse large B-cell lymphoma |
|
