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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression of microRNAs and their target mRNAs in hESC-derived cardiomyocyte clusters and in heart tissue_mRNA_data

ABSTRACT: Parallel transcription profiling of cardiomyocyte clusters derived from human embryonic stem cells. Both mRNA (this experiment) and miRNA (see E-MEXP-2655) transcription are measured and fetal and adult heart tissues are included as controls. This experiment was updated on 7th July 2011 to fix incorrect AH6 and FH3 files.

ORGANISM(S): Homo sapiens

SUBMITTER: Jane Synnergren

PROVIDER: E-MEXP-2654 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Global transcriptional profiling reveals similarities and differences between human stem cell-derived cardiomyocyte clusters and heart tissue.

Synnergren Jane J Améen Caroline C Jansson Andreas A Sartipy Peter P

Physiological genomics 20111213 4

It is now well documented that human embryonic stem cells (hESCs) can differentiate into functional cardiomyocytes. These cells constitute a promising source of material for use in drug development, toxicity testing, and regenerative medicine. To assess their utility as replacement or complement to existing models, extensive phenotypic characterization of the cells is required. In the present study, we used microarrays and analyzed the global transcription of hESC-derived cardiomyocyte clusters ...[more]

PMID: 22166955

Similar Datasets

Expression of microRNAs and their target mRNAs in hESC-derived cardiomyocyte clusters and in heart tissue_microRNA_data

Project description:Parallel transcription profiling of cardiomyocyte clusters derived from human embryonic stem cells. Both mRNA (E-MEXP-2654) and miRNA (this experiment) transcription are measured and fetal and adult heart tissues are included as controls. This experiment was updated on 7th July 2011 to fix incorrect AH6 and FH3 files

2011-03-30 | E-MEXP-2655 | biostudies-arrayexpress

Transcriptome dynamics of developing photoreceptors in 3-D retina cultures recapitulates temporal sequence of human cone and rod differentiation revealing cell surface markers and gene networks

Project description:To define molecular mechanisms underlying rod and cone differentiation, we generated H9 human embryonic stem cell line carrying a GFP reporter that is controlled by the promoter of cone-rod homeobox (CRX) gene, the first known marker of post-mitotic photoreceptor precursors. CRXp-GFP reporter in H9 line replicates endogenous CRX expression when induced to form self-organizing 3-D retina-like tissue. We define temporal transcriptome dynamics of developing photoreceptors during the establishment of cone and rod cell fate. Our studies provide an essential framework for delineating molecules and cellular pathways that guide human photoreceptor development and should assist in chemical screening and cell-based therapies of retinal degeneration. Undifferentiated CRXp-GFP HP hES cells and 3D-neural retina were collected at days 37, 47, 67 and 90 and dissociated into single cells. Cells were sorted at 4°C and by FACSAria (Becton Dickinson). GFP+ and GFP- cells were separately collected. Total RNA was extracted by RNA purification kit (Norgen Biotek) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). High quality of total RNA (RIN: 7.7-9.2) was subjected to libraries construction using 40-60 ng of total RNA as input. Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases. Fastq files were generated from reads passing chastity filter.

2015-08-03 | E-GEOD-67645 | biostudies-arrayexpress

Differentially expressed zinc finger proteins during human adipogenesis

Project description:To investigate the collective role of zinc finger proteins in adipogenesis, we induced adipogenesis using human mesenchymal stem cells (MSC) and compared the gene expression profiles using human Illumina beads arrays. We performed three independent experiments of time-series analysis (0h, 1h, 12h, 24h, 2d, 4d, 6d, 9d, 12d, 15d after induction of adipogenesis) in order to comprehensively capture the dynamic profiles of transcriptome during differentiation. Statistical filtering based on Analysis of Variance (ANOVA; p-value < 0.001, FDR 5%) and Gene Ontology classification using the Human Gene Nomenclature Database (HGNC) identified 618 out of 678 zinc finger proteins (ZFPs) that were significantly expressed during adipogenesis. Moreover, 34 out of 618 genes were differentially expressed more than 2-fold up or down regulated. The K-means clustering analysis further revealed four dynamic expression patterns: one gene in early-response, seven genes in transient, twenty genes in progressively-induced and four genes in the down-regulated, demonstrating the dynamic involvement of ZFPs in the process of adipocyte differentiation and maturation. Total RNA obteind from 10 different time points (0h, 1h, 12h, 24h, 2d, 4d, 6d, 9d, 12d, 15d) during adipogenesis from human Mesenchymal stem cell (MSC) to Adipocyte (ADP). Adipogensis was induced by the different cocktail of chemical compunds containing human-insulin, dexamethasone, indomethacin and IBMX.

2012-12-01 | E-GEOD-37836 | biostudies-arrayexpress

microRNA expression profiling among human embryonic stem cells, differerentiated EBs and adult cells

Project description:Human embryonic stem (hES) cells have unique features: self-renewal ability and pluripotency. They can be continuously cultured in undifferentiated state and give rise to cells and tissues of all three germ layers. Thus hES cells provide a resource not only for cell replacement therapy but also for studying human developmental biology. We aimed to identify the unique signature of miRNAs in human embryonic stem cells. Keywords: cell type comparison design We performed microRNA expression profiling on 3 passages from 2 different hES cell lines (WA09 (H9) and BG01v) and 4 passages from 1 hES cell line (TE06 (I6)), EBs samples derived from WA09 cells at 4 different time points with replicates, and 5 types of adult cells (HUVEC, HMVEC, UASMC NHA, and LFB).

2009-04-17 | E-GEOD-12229 | biostudies-arrayexpress

Transcription profiling by array of human neuroectoderm or embryonic stem cells after Pax6 knockdown

Project description:Stable Pax6 and Luciferase knockdown human embryonic stem cell lines (H9) were made through lentiviral infection. Two different Pax6 RNAi lines and two Luciferase RNAi lines were then differentiated to neuroectoderm cells for 6 days. mRNA pooled from these two individual lines were then subjected to gene expression profiling analysis using affymetrix U133 plus 2.0 array.

2010-07-01 | E-MEXP-2668 | biostudies-arrayexpress

Gene expresssion in human iPSC-derived neurons from normal and SPG3A donors

Project description:We performed RNA-seq experiments on two samples (cortical neurons and spinal motor neurons) from normal induced pluripotent stem cells (iPSCs), and another two samples (cortical neurons and spinal motor neurons) derived from SPG3A (an early onset form of hereditary spastic paraplegia) iPSCs. This initial experiment is to test the system and set up a baseline for future studies. Cortical projection neurons and spinal motor neurons were differentiated from same batch of iPSCs in parallel to minimize variations. The differentiation of cortical neurons and spinal motor neurons are based on protocols well-established in our group.

2019-03-25 | E-MTAB-7770 | biostudies-arrayexpress

Transcription profiling of human embryonic stem cells and neuroepithelial cells

Project description:Comparing gene expressing profile of human embryonic stem cells and neuroepithelial cells differentiated from human embryonic stem cells.

2009-11-08 | E-MEXP-2426 | biostudies-arrayexpress

Human embryonic stem cells, differerentiated EBs and adult cells

Project description:This SuperSeries is composed of the following subset Series: GSE12228: Gene expression profiling among human embryonic stem cells, differerentiated EBs and adult cells GSE12229: microRNA expression profiling among human embryonic stem cells, differerentiated EBs and adult cells Refer to individual Series

2009-04-17 | E-GEOD-12250 | biostudies-arrayexpress

Gene expression profiling among human embryonic stem cells, differerentiated EBs and adult cells

Project description:Human embryonic stem (hES) cells have unique features: self-renewal ability and pluripotency. They can be continuously cultured in undifferentiated state and give rise to cells and tissues of all three germ layers. Thus hES cells provide a resource not only for cell replacement therapy but also for studying human developmental biology. However, much work needs to be done to understand the molecular mechanisms responsible for the maintenance of the undifferentiatiation state and the differentiation process of human embryonic stem cells. Keywords: cell type comparison design We performed gene expression profiling on 3 separate passages from 3 different hES cell lines (WA09 (H9), TE06 (I6) and BG01v), EBs samples derived from WA09 cells at 3 different time points, and 5 types of adult cells (HUVEC, HMVEC, UASMC NHA, and LFB).

2009-04-17 | E-GEOD-12228 | biostudies-arrayexpress

The Dynamic Proteome of Oligodendrocyte Lineage Differentiation Features Planar Cell Polarity and Macroautophagy Pathways

Project description:Generation of oligodendrocytes (OLs) is a sophisticated multistep process, mechanistic underpinnings of which are not fully understood and demand further investigation. To systematically profile proteome dynamics during human embryonic stem cell (hESC) differentiation into OLs, we applied in-depth quantitative proteomics at different developmental stages and monitored changes in protein abundance using a multiplexed tandem mass tag (TMT) based proteomics approach. Findings: Our proteome data provided a comprehensive protein expression profile that highlighted specific expression clusters based on the protein abundances over the course of human OL lineage differentiation. The proteome profile of OL lineage cells revealed 378 proteins that were specifically up-regulated only in one differentiation stage. In addition, comparative pairwise analysis of differentiation stages demonstrated that abundances of 352 proteins differentially changed between consecutive differentiation time points. Our results highlighted the eminence of the planar cell polarity (PCP) signaling and autophagy (particularly macroautophagy) in the progression of OL lineage differentiation

2020-09-16 | PXD017649 | Pride

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