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Profiling ethanol-targeted transcription factors in human carcinoma cell-derived embryoid bodies.

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE67864 | GEO | 2015/04/15

SECONDARY ACCESSION(S): PRJNA281088

REPOSITORIES: GEO

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Profiling ethanol-targeted transcription factors in human carcinoma cell-derived embryoid bodies.

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.

2015-04-15 | E-GEOD-67864 | biostudies-arrayexpress

Microbiota, Appetite, and Malnutrition in Dutch Community-dwelling older adults

Project description:This concerns a cross-sectional cohort study of 356 Dutch community-dwelling older adults to study the association of the oral microbiota with poor taste, poor smell, poor appetite and undernutrition. Data-collection consisted of body measurements (incl. body weight, height, and body impedance analysis), extensive appetite and food frequency questionnaires, taste and smell tests, and a tongue swab. The oral microbiota composition was assessed with 16S rRNA sequencing.

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Project description:Interventions: Patients will be interviewed by phone about taste alterations. Information about the background of the patients, including gender, age and type and treatment of the GIST, will be collected from the patients electronic file. Primary outcome(s): What is the prevalence of taste and smell disturbances in GIST patients using TKIs? Study Design: N/A: single arm study, Open (masking not used), N/A , unknown, Other

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Project description:Next Generation Mendelian Genetics: Hereditary Neurological Disorders

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Next Generation Mendelian Genetics: Hereditary Neurological Disorders

Project description:Next Generation Mendelian Genetics: Hereditary Neurological Disorders

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Differential Expression of Immune Related Genes in Taste Buds of Fed and Fasted Mice

Project description:Purpose: The goal of this study is to compare the taste bud transcriptome of fasted and fed mice. By doing this we hope to gain more information about the taste bud transcriptome as well as determine transcriptional changes that may be linked with pre or post-ingestive states. Methods: Whole taste bud mRNA profiles of WT adult C57BL/6J mice were generated by Illumina HiSeq 2000 single end RNA sequencing. Prior to taste bud RNA isolation, mice were either food-deprived, fed, or given ad libitum access to standard rodent chow as a control. Sequence read quality was assesed using FastQC, and adapter sequences were trimmed using trimmomatic. Reads were then aligned to the GRCm38.p4 reference genome using Tophat2 followed by Cufflinks analysis, then gene level differential expression was conducted using Cuffdiff, and visualized via cummeRbund. Gene enrichment analysis of differentially expressed genes was performed using DAVID and Panther Gene Ontology. Results: We mapped about 30 million sequence reads per sample to the mouse genome, build GRCm38.p4, and identified 144 differentially expressed genes (FDR of 5%) between the taste buds of food-restricted, fed, and ad libitum control mice. Gene enrichment analysis of differentially expressed genes showed enrichment of pathways associated with cytokines, immunity, cytoskeletal structure, chaperone proteins, and protease inhibitors. Conclusions: Our study represents a detailed analysis of the murine taste bud transcriptome generated using RNA-seq technology. Our results highlight cellular pathways that may be differentially regulated in taste receptor cells during different pre/post-ingestive states. Additionally, as limited transcriptome information is available for taste buds, this dataset can serve as a resource for the discovery of genes novel to the taste bud.

2018-11-16 | GSE114624 | GEO

A comprehensive analysis of copy number variations in the human genome

Project description:Segmental copy number variations (CNVs) in the human genome are associated with developmental disorders and susceptibility to human diseases. More importantly, these variations may represent a major genetic component of our phenotypic diversity. In this study, using a whole genome array CGH assay, we identified 3,654 autosomal segmental CNVs, of which 800 appeared at a frequency of at least 3%. 77% of these frequent CNVs are novel. In the 95 individuals analyzed, the most diverse genomes differed by at least 9 Mb in size or varied by at least 266 loci in content. Approximately 68% of the 800 polymorphic regions overlap with genes, reflecting human diversity in senses (smell, hearing, taste, and sight), Rhesus phenotype, metabolism, and disease susceptibility. Intriguingly, 14 polymorphic regions harbor 21 of the known human microRNAs, raising the possibility of microRNAs’ contribution to phenotypic diversity in humans. This in depth survey of CNVs across the human genome provides a valuable baseline for studies involving human genetics. Keywords: array CGH, segmental copy number variations (CNVs)

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