More recently, a second generation array containing 7,000 spots (genes) was generated using cDNA libraries from all 40 developmental stages of F. heteroclitus [ 35].
First, simulated expression data for 1000 uncorrelated genes was generated for each subject using a random number generator derived from a normal distribution (mean = 0, variance = 2).
The list of 2C-related genes was generated by calculating the fold-change of 2C genes versus ESC genes, and taking the top 200 2C-associated genes.
To rank-order relevant germ-line alterations, a list of the Online Mendelian Inheritance in Man (OMIM) genes was generated for PHIAL (Supplementary Table S4 online).
A profile alignment of 16S rRNA genes was generated combining with the yeast 18S rRNA sequence from S. cerevisiae, which was used as an outgroup to root the species tree and then removed during tree reconciliation step.
By extracting the overlapped genes between in vivo and in vitro data, a core gene list including 541 unique genes was generated (Table S2).
Furthermore, by extracting the overlapped genes from in vivo and in vitro datasets, a core gene list including 541 unique genes was generated.
By integrating both in vivo and in vitro data, a combined gene list including 2237 unique genes was generated (Table S1).
An AnoGold dataset that contained EST-supported genes was generated [36].
By doing so, a list of potential off-targets for each of the individual genes was generated.
The genome alignment of the orthologous regions comprising the surE, pcm, nlpD and rpoS genes was generated by the multiple genome alignment software Mauve [62].
