Gene symbol were extracted from the HUGO Gene Nomenclature (HGNC) database [ 38] using the array probes description provided by GEO and manual searches.
To facilitate studies using the array at the probe level, we provide the genomic coordinates of probes containing novel 1000 Genomes SNPs as well as the transcript cluster ID, the probeset ID, each novel SNP's genomic position, and the SNP's position along the probe sequence in each population (Supplemental Tables S10, S11).
Despite these efforts, three different groups of transcriptional responses of the Pe/Pc ratio were detected depending on the species used to produce the array probe set.
Blast searches against the shotgun cDNA assemblies from SC and NBH embryos using the significant array probes resulted in further extension of some of the probe sequences.
A possible explanation for this higher sensitivity for low flows could be that the Vevo 770 uses a mechanically steered probe with a single element, as opposed to the array probe we used on Machine E in our study.
Thus, in order to establish an array normalization probe set, 1000 highly conserved genes were selected using in silico analysis of the nine completely sequenced SA genomes used to generate the array probes.
Custom CDFs (Chip Description File) from the BrainArray Project were used to map the array probes to 17,788 probe sets corresponding to individual Entrez Gene entries [ 49].
Although the techniques employed for performing DNA microarray experiments have been well established, improvements in the algorithms used for designing the array probes have been critical for advancing the reproducibility and accuracy of detecting the respective gene targets.
For probes classification and BOPs definition, the RELATION_TO_UCSC_CPG_ISLAND and the UCSC_REFGEN_NAME columns in the Illumina Infinium 450k annotation were used to subset the array probes in four classes and to group probes in BOPs.
The majority of the array probes used in this study are located in gene regions.
