GY118F downstream targets in iPS cells

This microarray was performed to gain insight in the downstream targets of GY118F in iPS cells. This array is part of the following paper to be published in Nature Communications: “JAK/STAT3 signalling is sufficient and dominant over antagonistic cues for the establishment of naïve pluripotency” by Anouk L. van Oosten, Yael Costa, Austin Smith & José C.R. Silva The samples analysed were: - GY118F iPS cells derived and maintained in N2B27 plus GCSF (t0, indicated in data as nlng t0 a), -same cells but from which GCSF was withdrawn for 12 or 24 hours (t-12, t-24, indicated in data as nlng t-12 a and nlng t-24 a) -and cells to which after withdrawal for 12 or 24 hours, subsequently GCSF was added back for 2 hours and 40 minutes (t-12+2h40m, t-24+2h40m, indicated in data as nlng t-12+2.4 a and nlng t-24+2.4 a). To obtain the data as presented in the manuscript the following was done:The values obtained for t0 were subtracted from t-12 and t-24. The values for t-12 and t-24 were subtracted from t-12+2h40m and t-24+th40m respectively. Subsequently the data was devided into genes that appeared to go down upon withdrawal of GCSF and up upon readdition and those with the converse gene expression pattern. Then a threshold of ≥1.4 fold change was applied. If a certain gene obeyed these criteria for all described comparisons, the gene was considered a potential downstream target. The fold change in expression was calculated by 2^absolute value of subtracted normalised data.