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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression of genetically related and unrelated human embryonic stem cell lines

ABSTRACT: Gene expression of sibling human ES cell lines are more similar to each other than unrelated cell lines. Undifferentiated human embryonic stem cells were used for analysis. We sought to determine whether genetic differences underly variations between different human ES cell lines. Sibling cell lines that are genetically closer than non-sibling cell provided the opportunity to determine this. We found that sibling cell lines are more similar in their gene expression patterns than unrelated cell lines. 16 Samples. HUES 55-58 are related, so are HUES 50 and HUES51, and so are HUES 62 and HUES 63.

ORGANISM(S): Homo sapiens

SUBMITTER: Kun Zhang

PROVIDER: E-GEOD-15294 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Optimal timing of inner cell mass isolation increases the efficiency of human embryonic stem cell derivation and allows generation of sibling cell lines.

Chen Alice E AE Egli Dieter D Niakan Kathy K Deng Jie J Akutsu Hidenori H Yamaki Mariko M Cowan Chad C Fitz-Gerald Claire C Zhang Kun K Melton Douglas A DA Eggan Kevin K

Cell stem cell 20090201 2

PMID: 19200798

Similar Datasets

Gene expression of genetically related and unrelated human embryonic stem cell lines

Project description:Gene expression of sibling human ES cell lines are more similar to each other than unrelated cell lines. Undifferentiated human embryonic stem cells were used for analysis. We sought to determine whether genetic differences underly variations between different human ES cell lines. Sibling cell lines that are genetically closer than non-sibling cell provided the opportunity to determine this. We found that sibling cell lines are more similar in their gene expression patterns than unrelated cell lines.

2009-03-20 | GSE15294 | GEO

Human testis-derived embryonic stem cell-like cells are not pluripotent, but possess potential of mesenchymal progenitors.

Project description:Comparison of whole genome gene expression profiles of human testis derived ES-like cells with pluripotent stem cells (human embryonic stem cell lines), adult human bone marrow derived mesenchymal stem cells and human dermal fibroblasts. Microarray study with total RNA of three testis derived ES-like cells clusters of one indivual (1) cultured in three different culture conditions A, B,C and embryoid bodies (EB) derived from them at 4, 7, 10, 14 and 18 days of suspension culture. Biological duplicates of human ES cell lines (HUES-1, GFP-hES-3),human bone marrow derived MSC (BMMSC1 and 2) and human dermal fibroblasts (DFB1 and 2) (LONZA CC-2511) at different passages were used as comparison groups.

2011-11-02 | E-GEOD-27203 | biostudies-arrayexpress

Transcript abundance in A-T-derived iPSC: Comparing isogenic cells to unrelated individual

Project description:Induced pluripotent stem cells (iPSC) were prepared from multiple subjects with Ataxia-telangiectasia (A-T). iPSC were prepared from activated T-cells using commercial Sendai virus to deliver reprogramming factors. ATM protein-expressing and non-expressing cultures would found in multiple sub-lines (sub-lines are generated from distinct founder colonies of cells) from a single subject (Q3). Genetic analysis determined that all sub-lines originated from the same subject and were likely the product of spontaneous reversion by gene correction. To compare gene expression profiles, three iPSC samples were assayed: (1) A reverted ATM+/- subline from subject Q3, (2) An ATM-/- subline from subject Q3, and (3) An iPSC line from an unrelated ATM-/- subject, Q1. Analysis reveals that the majority of significantly-different genes between the unrelated ATM-/- line (Q1SA) and the reverted ATM+/- line (Q3SC) was due to genetic variation between individuals. A more focused set of contrasting genes could be identified between the isogenic Q3-derived lines (Q3SA, ATM-/-, vs. Q3SC, ATM+/-). The 206 transcripts that are significantly different point to a differential regulation of p53-associated pathways.

2015-11-19 | GSE71878 | GEO

Transcript abundance in A-T-derived iPSC: Comparing isogenic cells to unrelated individual

2015-11-19 | E-GEOD-71878 | biostudies-arrayexpress

Homo sapiens

Project description:Genome wide analysis of bivalent domains in two HUES cell lines

| PRJNA255083 | ENA

Genome wide analysis of bivalent domains in two HUES cell lines

Project description:Human embryonic stem (HUES) cells are derived from early individual embryos with unique genetic properties. However, how their epigenetic status might affect their potential to differentiate toward specific lineages remains a puzzling question. Using ChIP-on-chip, the status of bivalent domains on gene promoters (i.e. H3K4 and H3K27 trimethylation) was monitored for both undifferentiated and BMP2 induced cardiac committed cells. A marked difference in the epigenetic profile of HUES cell lines was observed and this was correlated to the pattern of gene expression induced by BMP2 as well as to their potential to generate cardiac progenitors and differentiated myocytes. Thus, the epigenetic H3trimeK4 and H3trimeK27 prints generating bivalent domains on promoters, could be used to predict a preference in their differentiation toward a specific lineage.

2014-10-06 | GSE59328 | GEO

Early transcriptional changes linked to naturally occurring Huntington's disease mutations in human embryonic stem cells

Project description:Multiple human embryonic stem (ES) cell lines derived from blastocysts diagnosed as carrying the mutant huntingtin gene by pre-implantation diagnosis were used to explore early developmental changes in gene expression. How mutant huntingtin impacts on signalling pathways in the pre-symptomatic period has remained essentially unexplored in humans due to a previous lack of appropriate models. Total RNA was isolated from 10 human ES cell lines, 6 HD and 4 wild type control, and their neural stem cell (NSC) progeny.

2012-06-19 | E-GEOD-34201 | biostudies-arrayexpress

Expression data from rat pluripotent stem (PS) cells

Project description:Various pluripotent stem (PS) cells can be isolated from early developing embryos in mouse. Among these, two kinds of PS cells were isolated from mouse blastocysts: conventional embryonic stem (ES) cells with domed morphology that are maintained with LIF and BMP for self-renewal, and FAB-ES cells with flat morphology that need bFGF, activinA and BIO for self-renewal. Here, we report a novel PS cell line from rat blastocysts, which is distinguishable from conventional ES cells but is morphologically similar to mouse epiblast stem cell (EpiSC) lines. We used microarrays to detail the global program of gene expression of rES and rPS. Rat embryonic stem cell (ES) and rat flat pluripotent stem (fPS) cells were selected for RNA extraction and hybridization on Affymetrix microarrays. We analysed each sample for three replications.

2011-08-17 | E-GEOD-19820 | biostudies-arrayexpress

Pulmonary infection induces scarred lipidome influencing response to unrelated challenge

Project description:Pulmonary infection induces scarred lipidome influencing response to unrelated challenge

| PRJNA719826 | ENA

Gene expression levels in immortalized B cells from 131 unrelated CEPH-Utah grandparents treated under ER stress.

Project description:We used microarrays to examine gene expression levels from 131 unrelated CEPH-Utah grandparents with either DMSO or tunicamycin.

2013-03-28 | GSE36911 | GEO

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