8 protocols
AccessionType
bioassay_data_transformation
ID_REF =
VALUE = MAS5-calculated Signal intensity
ABS_CALL = This indicates whether a transcript is reliably detected (P) or not detected (A)
DETECTION P-VALUE = 'detection p-value', p-value is the significance level of the detection call
bioassay_data_transformation
ID_REF =
VALUE = MAS5-calculated Signal intensity
ABS_CALL = Presence or Absence of gene transcript in sample
DETECTION P-VALUE = significance value for detection of absolute calls
feature_extraction
The data was normalised with MAS 5.0 using the GCOS Software from Affymetrix using default settings. The normalization target was set to 500.
image_aquisition
The genechips were washed thoroughly after hybridisation and scanned using the Affymetrix GeneChip Scanner 3000 7G.
hybridization
The labelled cRNA obtained was fragmented and 15 microg of cRNA were hybridized to the Affymetrix HG-U133 plus 2.0 chip according to the protocols described by the manufacturer.
labeling
Biotinylated cRNA were prepared from 6 microg total RNA using the GeneChip Expression IVT Labelling kit from Affymetrix (USA) according to the manufacturers instructions.
nucleic_acid_extraction
HepG2 cells were grown to confluency and total RNA was isolated using Trizol (Invitrogen, CA, USA) according to the manufacturers instructions. The RNA so obtained was purified using the RNeasy Mini-kit (Qiagen, Germany)
nucleic_acid_extraction
HepG2 cells were grown to confluency and total RNA was isolated using Trizol (Invitrogen, CA, USA) according to the manufacturers instructions. The RNA so obtained was purified using the RNeasy Mini-kit (Qiagen, Germany)