Mygenechip custom array

The microarray used in this study is an Affymetrix MyGeneChip Custom Array (Affymetrix design number:FDACRONOa520845F) and was developed utilizing the whole genome sequences and 18 plasmids of 15 Cronobacter strains as previously described (Tall et al., 2015 (link); Yan et al., 2015b (link)).

The microarray used in this study is an Affymetrix MyGeneChip Custom Array (Affymetrix design number: FDACRONOa520845F) which utilizes the whole genome sequences of 15 Cronobacter strains, as well as 18 plasmids as described by Tall et al. (2015) (link). Each gene (19,287 Cronobacter gene targets) was represented on the array by 22 unique 25-mer oligonucleotide probes, as described by Jackson et al. (2011) (link) and Tall et al. (2015) (link). Genomic DNA from Cronobacter and phylogenetically related species as listed in Supplementary Table 7 was hybridized, washed in the Affymetrix FS-450 fluidics station, and scanned on the Affymetrix GeneChip Scanner 3000 (AGCC software) as described by Jackson et al. (2011) (link) and as modified by Tall et al. (2015) (link). All reagents for hybridization, staining and washing were made in conjunction with the Affymetrix GeneChip Expression Analysis Technical Manual.

The microarray used in this study was an Affymetrix MyGeneChip Custom Array (Affymetrix design number: FDACRONOa520845F), which utilizes the whole genome sequences of 15 Cronobacter strains, as well as 18 plasmids. These 15 strains encompassed all currently proposed species of Cronobacter. A ≥97% identity threshold level between gene homologs to positively predict allelic coverage was used to obtain genes that were represented on the array as described by Tall et al. [54 (link)]. Each gene (19,287 Cronobacter gene targets) was represented on the array by 22 unique 25-mer oligonucleotide probes, as described by Tall et al. [54 (link)].