Frozen samples homogenized on ice in the Trizol solution (GibcoBRL).
Growth protocol
Frozen samples
Extracted molecule
total RNA
Extraction protocol
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label
biotin
Label protocol
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA and hybridized on the HG U133 2.0 plus GeneChip.
Hybridization protocol
Following fragmentation, 15 mg of fragmented cRNA were hybridized to HG-U133 2.0 plus microarrays (Affymetrix, Inc.). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol
GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.
Description
Gene expression data from PTCL/U patient at diagnosis
Data processing
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
'signal' a meature of the abundance of a transcript (obtained using GCOS1.2); processed as GC-RMA and norrmalized per gene to median and per chip to 50th percentile in GeneSpring 3.7.1 (Agilent Tecnology)
ABS_CALL
the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
