|
| Status |
Public on Apr 10, 2009 |
| Title |
Germinal Center Centrocytes, sample 4 |
| Sample type |
RNA |
| |
|
| Source name |
Germinal Center Centrocytes from human tonsil
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD10-positive cell type: CD77-negative B-cells purified by magnetic cell separation.
|
| 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).
|
| |
|
| 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 |
CD10-positive CD77-negative B-cells purified by magnetic cell separation.
Gene expression data from purified germinal center centrocytes
|
| 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.
|
| |
|
| Submission date |
Jul 22, 2008 |
| Last update date |
Jan 10, 2023 |
| Contact name |
Laura Pasqualucci |
| E-mail(s) |
lp171@cumc.columbia.edu
|
| 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 |
|
| Relations |
| Reanalyzed by |
GSE86362 |
