Unknown,Transcriptomics,Genomics,Proteomics

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GY118F downstream targets in iPS cells

ABSTRACT: 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derived and maintained in N2B27 plus GCSF (t0, indicated in data as nlng t0 a), -same cells but from which GCSF was withdrawn for 12 or 24 hours (t-12, t-24, indicated in data as nlng t-12 a and nlng t-24 a) -and cells to which after withdrawal for 12 or 24 hours, subsequently GCSF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.

ORGANISM(S): Mus musculus

SUBMITTER: Jose Silva

PROVIDER: E-GEOD-36816 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The traditional method for studying cancer in vitro is to grow immortalized cancer cells in two-dimensional (2D) monolayers on plastic. However, many cellular features are impaired in these unnatural conditions and big alterations in gene expression in comparison to tumors have been reported. Three-dimensional (3D) cell culture models have become increasingly popular and are suggested to be better models than 2D monolayers due to improved cell-to-cell contacts and structures that resemble in vivo architecture. The aim of this study was to develop a simple high-throughput 3D drug screening method and to compare drug responses in JIMT1 breast cancer cells when grown in 2D, in polyHEMA coated anchorage independent 3D models and in Matrigel on-top 3D cell culture models. We screened 102 compounds with multiple concentrations and biological replicates for their effects on cell proliferation. The cells were either treated immediately upon plating or they were allowed to grow in 3D for four days prior to the drug treatment. Big variations in drug responses were observed between the models indicating that comparisons of culture model influenced drug sensitivities cannot be made based on effects of a single drug. However, we show with the 63 most prominent drugs that, in general, JIMT1 cells grown on Matrigel were significantly more sensitive to drugs than cells grown in 2D cultures, while responses of cells grown in polyHEMA resembled those of 2D. Furthermore, comparison of gene expression profiles of the cell culture models to xenograft tumors indicated that cells cultured in Matrigel and as xenografts most closely resembled each other. In this study we also suggest that 3D cultures can provide a platform for systematic experimentation of larger compound collections in a high-throughput mode and be used as alternatives for traditional 2D screens towards better comparability to in vivo state. Gene expression analysis of JIMT1 breast cancer cells cultured as xenografts for 43 days, in two dimensional cultures for seven days (2D7d), in polyHEMA three dimensional cell culture models for four and seven days (PH7d and PH7d), and in Matrigel three dimensional cultures for four and seven days (MG4d and MG7d). Two biological replicates was included for each sample.

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GY118F downstream targets in iPS cells

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