Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene expression profile of human embryonic stem cell-derived hepatocyte-like cells

ABSTRACT: The differentiation of pluripotent stem cells to hepatocyte-like cells offers the perspective of unlimited supply of human hepatocytes. However, the degree of differentiation of hepatic-like cells (HLC) remains controversial. To obtain an unbiased characterization, we performed a transcriptomics study using the Affymetrix Gene ChipÂ® HG-U133 plus 2.0, with HLC derived from embryonic and induced stem cells (ESC, hiPSC) from two different laboratories. Genome-wide gene expression profiles of ESC and HLC were compared to freshly isolated and up to 14 days cultivated primary human hepatocytes (see submission E-MTAB-3994) obtained under patient informed consent from three male donors. Three biological replicas were used for each ESC and HLC models. (associated data set: E-MTAB-3994 - Gene expression profile of human embryonic stem cell-derived hepatocyte-like cells in matrigel and recombinant laminins)

ORGANISM(S): Homo sapiens

SUBMITTER: Wolfgang Schmidt-Heck

PROVIDER: E-MTAB-4442 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Gene networks and transcription factor motifs defining the differentiation of stem cells into hepatocyte-like cells.

Godoy Patricio P Schmidt-Heck Wolfgang W Natarajan Karthick K Lucendo-Villarin Baltasar B Szkolnicka Dagmara D Asplund Annika A Björquist Petter P Widera Agata A Stöber Regina R Campos Gisela G Hammad Seddik S Sachinidis Agapios A Chaudhari Umesh U Damm Georg G Weiss Thomas S TS Nüssler Andreas A Synnergren Jane J Edlund Karolina K Küppers-Munther Barbara B Hay David C DC Hengstler Jan G JG

Journal of hepatology 20150525 4

<h4>Background & aims</h4>The differentiation of stem cells to hepatocyte-like cells (HLC) offers the perspective of unlimited supply of human hepatocytes. However, the degree of differentiation of HLC remains controversial. To obtain an unbiased characterization, we performed a transcriptomic study with HLC derived from human embryonic and induced stem cells (ESC, hiPSC) from three different laboratories.<h4>Methods</h4>Genome-wide gene expression profiles of ESC and HLC were compared to freshl ...[more]

PMID: 26022688

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Project description:The anaerobic Gram-positive bacterium Propionibacterium acnes is a human skin commensal, but is occasionally associated with inflammatory diseases. Recent work has indicated that evolutionary distinct lineages of P. acnes play etiologic roles in disease while others are associated with health. To shed light on the molecular basis for differential strain properties, we carried out genomic and transcriptomic analysis of distinct P. acnes strains. We sequenced the genome of the P. acnes strain 266, a type I-1a sequence type (ST) 18 strain. Comparative genome analysis of strain 266 and four other P. acnes strains revealed that overall genome plasticity is relatively low; however, a number of island-like genomic regions, encoding a variety of putative virulence-associated and fitness traits, differ between phylotypes. Comparative transcriptome analysis revealed that 225 genes of strain KPA171202 (type I-2, ST34) were differentially transcribed in strain 266 during exponential growth. 47% of these genes belong to the strain-specific gene content of strain KPA171202, indicating that strain-specific functions are utilized. Next, we studied differential expression during exponential and stationary growth phases. Genes encoding components of the energy-conserving respiratory chain as well as secreted and virulence-associated factors were transcribed during the exponential phase, while the stationary growth phase was characterized by up-regulation of genes involved in the stress response and amino acid metabolism. Taken together, our data highlight the genomic basis for strain diversity and identify, for the first time, the transcribed part of the genome, underling the important role active growth plays in the inflammatory activity of P. acnes. We argue that the disease-causing potential of different P. acnes strains is not only determined by variable genome content but also, and to a greater degree, by variable transcriptomes. Microarray experiments were performed as dual-color hybridizations. In order to compensate specific effects of the dyes and to ensure statistically relevant data analysis, a color-swap dye-reversal was performed. Two different labeling methods were applied. RNA labeling was performed with the two color Quick Amp Labeling Kit (Agilent Technologies) using FullSpectrum MultiStart Primer for T7 IVT RNA Amplification (BioCat GmbH, Heidelberg, Germany) as random T7 labeling. Alternatively, the total RNA samples were amplified with the TransPlex Whole Transcriptome Amplification Kit (Sigma-Aldrich, Munich, Germany) and labeled with BioPrime Plus Array CGH Indirect Genomic Labeling System (Invitrogen, Karlsruhe, Germany) as WTA BioPrime indirect. Both methods were compared and combined for final data analysis.

Dataset Information

Gene expression profile of human embryonic stem cell-derived hepatocyte-like cells

Publications

Gene networks and transcription factor motifs defining the differentiation of stem cells into hepatocyte-like cells.

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