|
| Status |
Public on May 05, 2011 |
| Title |
SU-DHL4, untreated, rep1 |
| Sample type |
RNA |
| |
|
| Source name |
SU-DHL4
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SU-DHL4
cell type: B-cell lymphoma cells
|
| Growth protocol |
Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
SU-DHL4_untreated_1
|
| Data processing |
Expression arrays were analyzed using the statistical programming environment R and Bioconductor. Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
We defined a probe set as significantly regulated if (a) at least a two-fold change was observed and (b) the BH-corrected p-value was below 0.05.
|
| |
|
| Submission date |
Mar 21, 2011 |
| Last update date |
May 05, 2011 |
| Contact name |
Volkhard Seitz |
| E-mail(s) |
[email protected]
|
| Organization name |
Charité Universitätsmedizin
|
| Department |
Institute of Pathology
|
| Street address |
Hindenburgdamm 30
|
| City |
Berlin |
| ZIP/Postal code |
12200 |
| Country |
Germany |
| |
|
| Platform ID |
GPL96 |
| Series (2) |
| GSE21254 |
Classical Hodgkin lymphoma shows epigenetic features of an abortive plasma cellular differentiation |
| GSE28079 |
Classical Hodgkin lymphoma shows epigenetic features of an abortive plasma cellular differentiation: expression of PCM vs. B-cell lines |
|
| Relations |
| Reanalysis of |
GSM531238 |
