|
| Status |
Public on Sep 12, 2012 |
| Title |
c_D_1004 |
| Sample type |
genomic |
| |
|
| Source name |
fresh frozen tumor sample
|
| Organism |
Homo sapiens |
| Characteristics |
type: primary DLBCL
|
| Treatment protocol |
10-20 x 20mm sections from frozen tumor specimens from newly diagnosed previously untreated diffuse large B-cell lymphomas and peripheral blood lymphocytes from normal donors were directly transferred to extraction buffers.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For total RNA, frozen tissue sections were homogenized in Trizol and RNA was extracted according to standard protocols. For high molecular weight genomic DNA, frozen tissue sections were homogenized in 1 ml of G2-buffer supplemented with 2 ml RNase (Qiagen). Subsequently, DNA was extracted using the genomic buffer kit with 20/G genomic-tips (Qiagen) following the manufacturer's recommendations.
|
| Label |
biotin
|
| Label protocol |
PCR products were labeled with a single biotin according to the Affymetrix protocol.
|
| |
|
| Hybridization protocol |
Following fragmentation, biotinylated PCR fragments were hybridized overnight according to the Affymetrix protocol.
|
| Scan protocol |
GCS3000 (Affymetrix)
|
| Description |
LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_F02_609646
|
| Data processing |
The raw cel files were converted into probeset-specific expression values using Affymetrix MAS5 summarization method as implemented in the BioConductor package simpleaffy (Gentleman et al., 2004). All samples were scaled to have a mean expression level of 100. Copy number values were inferred from raw CEL files with a GenePattern pipeline which runs the following modules: SNPFileCreator, CopyNumberInference, RemoveCopyNumberOutliers, DivideByNormals and Quality Control.
|
| |
|
| Submission date |
Dec 07, 2011 |
| Last update date |
Sep 21, 2014 |
| Contact name |
Björn Chapuy |
| E-mail(s) |
Bjoern_Chapuy@dfci.harvard.edu
|
| Phone |
+1-617-632-3881
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Onology
|
| Lab |
Shipp Lab
|
| Street address |
450 Brookline Ave.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE34171 |
Integrative Analysis of a series of newly diagnosed Diffuse Large B-cell Lymphomas (DLBCLs) |
|
| Relations |
| Reanalyzed by |
GSM1509162 |
