Early passages of cells were cultured in a humidified atmosphere containing 5% of CO2 in Dulbecco's modified Eagle's medium (DMEM) (Cellgro, Herndon, VA), supplemented with 10% Fetal Bovine Serum (ATCC, Manassas, VA), 1% penicillin (Cellgro), and kept in a humidified incubator (Kendro Lab, New Town, CT) at 37°C.
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracted from fibroblasts of UIP histology lung tissue or normal histology lung tissue using TRIzol reagent (GIBCO-BRL, Gaithersburg, MD) according to the manufacturer protocol for RNA extraction and purification. RNA was stored at - 80°C until use.
Label
Biotin
Label protocol
The extracted total RNA was used as a template to generate double-stranded cDNA and biotin-labeled cRNA, as recommended by the manufacturer of the arrays.
Hybridization protocol
Fragmented cRNA was hybridized to Codelink Uniset I slides. After hybridization, arrays were washed and stained with streptavidin-AlexaFluor 647.
Scan protocol
The arrays were scanned using a Genepix 4000B microarray scanner. Images were analyzed using Codelink expression II analysis suite, and visually inspected for defects and quality control parameters as recommended by the manufacturer.
Description
8396 genes that had an Entrez gene ID demonstrate minimal changes in gene expression between fibroblasts from UIP histology lung tissue and normal histology lung tissue. Among them, 236 genes were substantially changed (TNoM=0 and t-test p-value <0.05).
Statistical analysis was performed using Scoregene gene expression package, and data visualization was performed using Genomica and Spotfire Decision Site 8.0.
