Transcriptomic and Genomic Analysis of Soybean

The above RNA extracts were reverse transcribed to synthesize double stranded complementary DNA (cDNA). After purification of the double-stranded cDNA products, the sample was transcribed in vitro to generate Biotinylated complementary RNAs (cRNAs), followed by purification and fragmentation. The purified and fragmented cRNAs were then hybridised to the Affymetrix Soybean Gene Chip array (ThermoFisher Scientific, Lutterworth, UK). The scanned arrays produced CEL raw data files that were loaded onto Genespring GX version 13.1 (Agilent Genomics, Santa Clara, CA, USA) for further analysis. The extraction of genomic DNA (gDNA) from the two genotypes was performed using the DNA extraction Qiagen kit according to manufacturer’s instructions. Extracted DNA was labelled and hybridised to the Affymetrix Soybean TEST3 array and resulted in the generation of gDNA cell-intensity files (CEL files), after scanning. To identify probe pairs that efficiently hybridise to the gDNA, a series of user defined threshold values were evaluated for the signal intensity. The perfect match (PM) probes were selected for interpreting the GeneChip arrays challenged with RNA from the species of interest [35 (link)].