Affymetrix clariom d arrays

RNA integrity was evaluated using the Agilent Bioanalyzer 2100 with the RNA 6000 Nano kit (Agilent Technologies). For microarray analysis, 200 ng of isolated RNA samples was applied and hybridization was performed as described previously [15 (link)]. Hybridization was carried out on Affymetrix Clariom^TM D Arrays according to the instructions of the manufacturer (Thermo Fisher Scientific).

RNA integrity was analyzed using the Agilent Bioanalyzer 2100 with the RNA Pico chip kit (Agilent Technologies). 200 ng of isolated RNAs were subjected to microarray hybridization as described in [35 (link)]. Hybridization was performed on Affymetrix Clariom^TM D Arrays according to the manufacturer’s instructions (Thermo Fisher).
Analysis of the microarray data was conducted with the provided Transcriptome Analysis Console Software from Thermo Fisher (Version 4.0.1, Waltham, USA). The analysis included quality control, data normalization, and statistical testing for differential expression (Limma). Transcripts were considered as significantly differentially expressed with a fold change (FC) higher than 2 or smaller −2, false discovery rate (FDR) < 0.05, and p < 0.05. The pathway analyses were conducted based on a gene set enrichment analysis using Fisher’s Exact Test (GSEA) on the Wiki-Pathways database. Only significant pathways have been selected.