BioProject

Gene expression profiling reveals mesoderm lineage-specific genes were more significantly regulated with the most prominent regulated DEGs were identified in adipose tissue. More...

Gene expression profiling reveals mesoderm lineage-specific genes were more significantly regulated with the most prominent regulated DEGs were identified in adipose tissue. We evaluated the effects of Tsuruazuki extract on human amniotic epithelial stem cells. We performed an untargeted whole-genome transcriptome analysis to explore functionality of Tsuru in a stem cell-based tool. Overall design: According to the manufacturer's guide, the RNA was extracted using Isogen kit (Nip-pon Gene Co. Ltd., Japan). Then, RNA quantity and quality were determined using the NanoDrop 2000 spectrophotometer (ThermoScientific, USA). DNA microarray analysis was conducted on control and Tsuru-treated hAESC samples using the GeneChip WT PLUS Reagent Kit (ThermoFisher Scientific) and GeneChip™ Hybridization, Wash and Stain Kit (ThermoFisher Scientific) following the manufacturer's instructions. In brief, complementary DNA (cDNA) was synthesized from 100 ng of RNA solutions. cRNA was synthesized from in vitro transcription of cDNA and then purified and reverse transcribed. Finally, single-stranded cDNA (ss-cDNA) was synthesized, purified, fragmented, and labeled following the manufacturer's instructions. Cartridge Array Hybridization was performed using the Clariom S array (Human; ThermoFisher Scientific) on the GeneChip™ Fluidics Station (ThermoFisher Scientific). Scanning was performed using GeneChip Scanner (ThermoFisher Scientific). The raw image data was obtained using the Transcriptome Analysis Console (TAC) software (ver. 4.0.2, ThermoFisher Scientific) and raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above back-ground (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7. Finally, genes that passed the filter criteria of p value < 0.05 (one-way between-subjects ANOVA) and fold change > 1.1 (in linear space) were considered as differentially expressed genes (DEGs). Less...