Whole genome transcriptomics of simvastatin treatment in Mesodermal Progenitor Cells

ABSTRACT: Whole-genome transcriptomic analysis of MPCs treated for 2 days or 17 days with simvastatin 1 uM and of the corresponding DMSO-treated controls was performed using MPCs treated 2 days or 17 days, respectively. Total RNA was isolated using the RNeasy Mini kit (Qiagen) with DNAse I digestion. RNA concentration and quality were measured using the NanoDrop ND-1000A spectrophotometer. RNA integrity was evaluated on Agilent Bioanalyzer 2100. Using 200 ng of RNA as input material, sense strand cDNA was generated with Ambion WT expression kit (PN 900671). The Affymetrix GeneChip WT Labeling Kit (PN 900671) was then used to fragment and biotin label sense target for hybridization onto Affymetrix Human Gene 1.1 ST array plates, containing 36,079 RefSeq transcripts. Hybridization Cocktail was prepared according to Affymetrix standard protocol for Gene 1.1 STArray plates. The Gene Titan Instrument system was used for hybridization, washing, staining and scanning. Gene array processing was performed at the Bioinformatics and Expression Analysis (BEA) core facility, Karolinska Institutet. Data analysis of the Affymetrix array plates results was performed with Affymetrix Expression Console (EC, version 1.1) using the following methods: (i) summarization: PLIER, (ii) background correction: PM-GCBG and (iii) normalization: Global Median. Expression levels in the treatment groups were compared to the control groups using Students t-test (2-sided, unpaired) analysis. For each time point, a list of differentially expressed (DE) genes was generated, using 2 and 0.05 as fold change and p-value cut-off values, respectively.

INSTRUMENT(S): NA, NanoDrop ND-1000A spectrophotometer. Agilent Bioanalyzer 2100, Affymetrix GeneChip WT Labeling Kit, Gene Titan Instrument system

ORGANISM(S): Homo sapiens

SUBMITTER: Isabel Barragan 

PROVIDER: E-MTAB-2753 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress