|
Status |
Public on Apr 10, 2009 |
Title |
DLBCL biopsy, sample 2195 |
Sample type |
RNA |
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|
Source name |
DLBCL frozen biopsy
|
Organism |
Homo sapiens |
Characteristics |
tissue: lymph node tumor
|
Treatment protocol |
Not applicable
|
Growth protocol |
Lymphoma biopsies were snap frozen in liquid nitrogen or embedded in OCT compound followed by flash freezing in liquid nitrogen
|
Extracted molecule |
total RNA |
Extraction protocol |
Tissue samples were homogenized in Trizol and extraction of total RNA was performed according to the manufacturer's instructions.
|
Label |
Biotin
|
Label protocol |
Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
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|
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Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for at least 16 hr at 45C on GeneChip Human Genome Array U133Plus_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.
|
Description |
frozen biopsy of lymph node tumor Gene expression data from primary DLBCL biopsy
|
Data processing |
Data were normalized using MAS5 and subsequently log2 transformed. For Gene Set Enrichment Analysis (GSEA), probesets were first filtered out if mean, mu<50, or coeffient of variation, CV<0.3 (as assessed in 259 B cell-related gene expression profiles from U133Plus_2 arrays) ; these probes do not appear in the attached Matrix.
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|
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Submission date |
Mar 30, 2009 |
Last update date |
Jan 10, 2023 |
Contact name |
Laura Pasqualucci |
E-mail(s) |
[email protected]
|
Organization name |
Columbia University
|
Department |
Institute for Cancer Genetics
|
Street address |
1130 St Nicholas Avenue
|
City |
New York |
State/province |
NY |
ZIP/Postal code |
10032 |
Country |
USA |
|
|
Platform ID |
GPL570 |
Series (1) |
GSE12195 |
Mutations of multiple genes deregulate the NF-kB pathway in diffuse large B cell lymphoma |
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