The pluripotency of newly developed human induced pluripotent stem cells (iPSCs) is usually characterized by physiological parameters; i.e., by their ability to maintain the undifferentiated state and to differentiate into derivatives of the three germ layers. Nevertheless, a molecular comparison of physiologically normal iPSCs to the gold standard of pluripotency, embryonic stem cells (ESCs), often reveals a set of genes with different expression and/or methylation patterns in iPSCs and ESCs. To evaluate the contribution of the reprogramming process, parental cell type, and fortuity in the signature of human iPSCs, we developed a complete isogenic reprogramming system. We performed a genome-wide comparison of the transcriptome and the methylome of human isogenic ESCs, three types of ESC-derived somatic cells (fibroblasts, retinal pigment epithelium and neural cells), and three pairs of iPSC lines derived from these somatic cells. Our analysis revealed a high input of stochasticity in the iPSC signature that does not retain specific traces of the parental cell type and reprogramming process. We showed that five iPSC clones are sufficient to find with 95% confidence at least one iPSC clone indistinguishable from their hypothetical isogenic ESC line. Additionally, on the basis of a small set of genes that are characteristic of all iPSC lines and isogenic ESCs, we formulated an approach of the best iPSC line selection and confirmed it on an independent dataset.
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Sex, Specimen part
View SamplesThe pluripotency of newly developed human induced pluripotent stem cells (iPSCs) is usually characterized by physiological parameters; i.e., by their ability to maintain the undifferentiated state and to differentiate into derivatives of the three germ layers. Nevertheless, a molecular comparison of physiologically normal iPSCs to the gold standard of pluripotency, embryonic stem cells (ESCs), often reveals a set of genes with different expression and/or methylation patterns in iPSCs and ESCs. To evaluate the contribution of the reprogramming process, parental cell type, and fortuity in the signature of human iPSCs, we developed a complete isogenic reprogramming system. We performed a genome-wide comparison of the transcriptome and the methylome of human isogenic ESCs, three types of ESC-derived somatic cells (fibroblasts, retinal pigment epithelium and neural cells), and three pairs of iPSC lines derived from these somatic cells. Our analysis revealed a high input of stochasticity in the iPSC signature that does not retain specific traces of the parental cell type and reprogramming process. We showed that five iPSC clones are sufficient to find with 95% confidence at least one iPSC clone indistinguishable from their hypothetical isogenic ESC line. Additionally, on the basis of a small set of genes that are characteristic of all iPSC lines and isogenic ESCs, we formulated an approach of the best iPSC line selection and confirmed it on an independent dataset.
No associated publication
Sex, Specimen part
View SamplesAlteration in gene expression accompanying initial stages of allopolyploidy is a prominent feature in plants, but its spectrum and model are highly idiosyncratic. We used multi-colour GISH to identify individuals from two nascent allohexaploid wheat lines between Triticum turgidum and Aegilops tauschii, which had a transgenerationally stable chromosomal constitution mimicking that of common wheat. We performed genomewide analysis of gene expression for these plants along with their parental species using the Affymetrix GeneChip Wheat Genome-Array. Comparison with parental species coupled with inclusion of empirical mid-parent values (MPVs) revealed two patterns of alteration in gene expression in the allohexaploid lines: parental dominance expression and nonadditive expression. Genes involved in each altered pattern could be classified into three distinct groups, stochastic, heritable and persistent, based on their transgenerational heritability and inter-line conservation. Whereas both altered patterns of gene expression showed a propensity of inheritance, identity of the involved genes is stochastic, consistent with the involvement of diverse Gene Ontology (GO) terms. Nonetheless, those genes showing nonadditive expression exhibited a significant enrichment for vesicle-function. Our results suggest global alteration in gene expression conditioned by nascent allopolyploidy likely play functional roles in stabilization and establishment of the newly formed plants, and consequential to evolution.
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Specimen part
View SamplesWe have found that overexpression of OsNPR1, a master gene for SAR in rice, greatly enhanced disease resistance. However, the growth and development of the OsNPR1 overexpression (OsNPR1-OX) lines were restrained and the mechanism remained elusive.
The Systemic Acquired Resistance Regulator OsNPR1 Attenuates Growth by Repressing Auxin Signaling through Promoting IAA-Amido Synthase Expression.
Specimen part
View SamplesOur previous studies have clearly demonstrated the roles of hPCL3s (PHF19) in the migration, invasion and metastasis of HCC cells. The microarray analysis was performed to screen the differentially expressed genes in the PVTT/hPCL3s
No associated publication
Specimen part
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Coordinated regulation of hepatic and adipose tissue transcriptomes by the oral administration of an amino acid mixture simulating the larval saliva of Vespa species.
Sex, Specimen part
View SamplesTo study the development mechanisms of type 2 diabetes, we examined multi-tissues' expression profiles of outbred mice fed with a high-fat diet (HFD) or regular chow at week 1, 9, and 18 and performed a novel dual eigen-analysis.
A Novel Dual Eigen-Analysis of Mouse Multi-Tissues' Expression Profiles Unveils New Perspectives into Type 2 Diabetes.
Sex, Specimen part
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Quantitative deviating effects of maple syrup extract supplementation on the hepatic gene expression of mice fed a high-fat diet.
Sex, Specimen part
View SamplesVAAM stands for an amino acid mixture simulating the composition of Vespa, a hornet larval saliva. We conducted a comparative study on metabolism-regulatory roles of VAAM, casein-simulating amino acid mixture (CAAM), and pure water on murine hepatic and adipose tissue transcriptomes. Mice were orally fed VAAM solution ( 0.675 g/ kg BW = 2% of food-derived amino acids = 0.38% of total food energy/ day), CAAM solution ( 0.675 g / kg BW/ day) or water under ad libitum for five days. Hepatic transcriptome comparison of VAAM, CAAM and water-treated groups revealed a VAAM-specific regulation of the metabolic pathway, i.e., the down-regulation of glycolysis and fatty acid oxidation, and up-regulation of poly unsaturated fatty acid synthesis and glycogenic amino acids utilization in TCA cycle. Similar transcriptomic analysis of white and brown adipose tissues (WAT and BAT) suggested the up-regulation of phospholipid synthesis in WAT and the negative regulation of cellular processes in BAT. Because these coordinated regulations of tissue transcriptomes implicated the presence of upstream signaling common to these tissues, we conducted Ingenuity Pathways Analysis of these transcriptomes with the results that estrogenic and glucagon signals seemed to be activated in liver and WAT as well as beta-adrenergic signaling did in the three tissues by administration of VAAM. Our data provide a clue to understanding the role of VAAM in metabolic regulation of multiple tissues.
Coordinated regulation of hepatic and adipose tissue transcriptomes by the oral administration of an amino acid mixture simulating the larval saliva of Vespa species.
Sex, Specimen part
View SamplesVAAM stands for an amino acid mixture simulating the composition of Vespa, a hornet larval saliva. We conducted a comparative study on metabolism-regulatory roles of VAAM, casein-simulating amino acid mixture (CAAM), and pure water on murine hepatic and adipose tissue transcriptomes. Mice were orally fed VAAM solution ( 0.675 g/ kg BW = 2% of food-derived amino acids = 0.38% of total food energy/ day), CAAM solution ( 0.675 g / kg BW/ day) or water under ad libitum for five days. Hepatic transcriptome comparison of VAAM, CAAM and water-treated groups revealed a VAAM-specific regulation of the metabolic pathway, i.e., the down-regulation of glycolysis and fatty acid oxidation, and up-regulation of poly unsaturated fatty acid synthesis and glycogenic amino acids utilization in TCA cycle. Similar transcriptomic analysis of white and brown adipose tissues (WAT and BAT) suggested the up-regulation of phospholipid synthesis in WAT and the negative regulation of cellular processes in BAT. Because these coordinated regulations of tissue transcriptomes implicated the presence of upstream signaling common to these tissues, we conducted Ingenuity Pathways Analysis of these transcriptomes with the results that estrogenic and glucagon signals seemed to be activated in liver and WAT as well as beta-adrenergic signaling did in the three tissues by administration of VAAM. Our data provide a clue to understanding the role of VAAM in metabolic regulation of multiple tissues.
Coordinated regulation of hepatic and adipose tissue transcriptomes by the oral administration of an amino acid mixture simulating the larval saliva of Vespa species.
Sex, Specimen part
View Samples