Project description:A total of 493 differentially expressed genes were identified in response to 50 mM ethanol exposure, in which 111 of them were up-regulated and 382 were down-regulated. Gene ontology term enrichment analysis revealed that the genes are involved in the important biological processes like neurological system process, cognition, behavior, sensory perception of smell, taste and chemical stimuli and synaptic transmission. In consistent, disease enrichment chart showed relevant categories like neurological diseases, developmental disorders, skeletal and muscular disorders, connective tissue disorders. Furthermore, we have shorted out a group of 26 genes that encode transcription factors. We validated relative gene expression of several transcription factors from the list by quantitative real time PCR. We hope that our study substantially contributes to the understanding of the molecular mechanism underlying the pathology of alcohol mediated anomalies and ease further research. Our aim was to provide a profile of important regulator that exerts ethanol related genomic alteration. For this, we have analyzed gene expression pattern of human carcinoma cell derived embryoid bodies in absence or presence of ethanol. A cDNA microarray analysis was used to profile mRNA expression in embryoid bodies at day 7 with or without ethanol treatment.
Project description:time-course experiment with embryoid bodies of CGR8 mouse embryonic stem cells ; in the whole time-series RNA from 0 days old embryoid bodies were hybridized against RNA from 3 days and 10 days old embryoid bodies Keywords = embryoid bodies Keywords = mouse Keywords = time-course Keywords = oligonucleotide array Keywords: time-course
Project description:16 embryonic stem cell (ESC) samples (8 groups in duplicate) were processed for microarray analysis using the Affymetrix Mouse Genome 430 2.0 GeneChip. The samples included the parental Ainv15 ESC line (1) undifferentiated (Ainv15 ESC), (2) differentiated for 3 days as embryoid bodies (Ainv15 EB3) or (3) for 10 days as embryoid bodies (Ainv15 EB10). The remaining samples included tetracycline inducible Ngn3 ESC line derived from the parental Ainv15 ESC line (4) after differentiation and addition of doxycycline for 3 days without embryoid body formation (Ngn3 ES3 ON), (5 and 6) after differentiation as embryoid bodies for 3 days with (Ngn3 EB3 ON) or without (Ngn3 EB3 OFF) doxycycline, and (7 and 8) after differentiation as embryoid bodies for 10 days with (Ngn3 EB10 ON) or without (Ngn3 EB10 OFF) doxycycline.
Project description:Progenitor cells require coordinated expression of lineage-specific genes to regulate differentiation into daughter cell types. Hopx labels cardiac progenitors that are commited to the cardiac myocyte lineage. Hopx-deficiency leads to thin myocardium in approximately mid-gestation lethality in approximately 50% of embryos (secondary to thin myocardium and presumed cardiac rupture). Hopx-/- EBs display impaired myogenesis during cardiac differentiation. ChIP-seq and RNA expression analysis suggests that Hopx down regulates Wnt signaling by directly occupying and repressing wnt ligand genes. Analysis of embryoid bodies on day 8 of cardiac differentiation. RNA was made of from Hopx +/- embryoid bodies or Hopx -/- embryoid bodies treated with 12.5 uM XAV939. Heterozygous embryoid bodies included 0 uM XAV939, a well-characterized, known Wnt inhibitor. Embryonic stem cell lines were derived from littermate mouse blastocysts. Results provide insight into gene programs regulated by Hopx in cardiac development.
