10 protocols
AccessionNameType
P-MTAB-28209
specified_biomaterial_action
Standard cell lysis protocol for mRNA processing workflows.
P-MTAB-28215
bioassay_data_transformation
Data processing were implemented in the R statistical environment. Raw RNA expression data was analyzed using the affy and gcrma packages of the Bioconductor suite of microarray analysis tools available in the R statistical environment. GCRMA background correction and quantile normalization were used to generate probe set expression values.
P-MTAB-28214
feature_extraction
Command Console Software (Affymetrix) was used to automatically grid the DAT files and create the CEL files (probe cell intensity data).
P-MTAB-28213
image_acquisition
The arrays were scanned and the raw image data was saved in DAT files.
P-MTAB-28212
hybridization
The biotin-labeled RNA was hybridized on Affymetrix U133 Plus 2.0 microarrays. The wash and stain procedures were performed according to Affymetrix protocols (GeneChip(R) Expression Wash, Stain and ScanUser Manual, Affymetrix).
P-MTAB-28211
labeling
Based on GeneChip(R) 3' IVT Express Kit - Affymetrix and according to suppliers standard protocols.
P-MTAB-28207
compound_based_treatment
Three exposure conditions were applied: 1. Initial treatment with standard culture medium for 24 hours, second treatment after washing with standard culture medium for either 2, 4, 6, or 8 hours 2. Initial treatment with inhibitor for 24 hours, second treatment after washing with inhibitor for either 2, 4, 6, or 8 hours 3. Initial treatment with inhibitor for 24 hours, second treatment after washing with standard culture medium for either 2, 4, 6, or 8 hours
P-MTAB-28210
nucleic_acid_extraction
Total RNA was extracted using RNeasy Microkit (Qiagen).
P-MTAB-28208
harvest
Cells were harvested after the second treatment and immediately put on ice.
P-MTAB-28206
grow
Normal human bronchial epithelial cells (Lonza Walkersville, Inc.) were cultured in standard growth medium (Clonetics medium, Lonza Walkersville, Inc.) for 24 hours