8 protocols
AccessionType
bioassay_data_transformation
ID_REF = VALUE = log2 MAS5 signal intensity CALL =
feature_extraction
Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software (Agilent technologies, Santa Clara, CA, US).
image_aquisition
Slides were scanned by GeneChip� Scanner 3000 and Command Console Software 3.1 with default settings.
hybridization
Array hybridization and wash was performed using GeneChip� Hybridization, Wash and Stain Kit in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.
labeling
Using Affymetrix GeneChip 3’IVT Express Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) to obtain biotin labeled cRNA according to manufacturer's instruction.
nucleic_acid_extraction
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018,Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
grow
Macrophages from peritoneal fluid after Percoll isolation was cultured in RPMI 1640
specified_biomaterial_action
PBS washing