Expression data from NcGFP ki/+, NcGFP ki/ki and wt (W4) ES cells
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ABSTRACT: We generated a gene replacement allele of the E-cadherin locus that express an N-cadherin-GFP fusion in ES cells. Expression profiles of homozygous and heterozygous knock-in ES cells were analyzed in comparison to wt ES cells. The GEO Samples were compared to published data of E-cadherin knock-out ES cells (ArrayExpress, accession number E-MEXP-2836). The comparison data are linked below.
Project description:We generated a gene replacement allele of the E-cadherin locus that express an N-cadherin-GFP fusion in ES cells. Expression profiles of homozygous and heterozygous knock-in ES cells were analyzed in comparison to wt ES cells. The GEO Samples were compared to published data of E-cadherin knock-out ES cells (ArrayExpress, accession number E-MEXP-2836). The comparison data are linked below. RNA was extracted from two independent experiments per genotype, data analysis was performed using the R/Bioconductor Limma software. Quality of the data set was controlled by the simpleaffy package and normalized by quantile normalization with the GCRMA alogrithm.
Project description:In order to identify the effects of the knock-down of the gene of interest on the mouse ES transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the knock-down cell line. Transcriptome analysis of the knock-down transgenic mouse ES cell line. The knock-down cell line (shE13) was generated by stably expressing a specific short-hairpin RNA against E13 sequence thus knocking-down E13 expression in parental mouse ES cell line E14Tg2a.4 (E14, Hooper M et al., 1987). The specific mouse gene knocked down in the ES cell line is E130012A19Rik.
Project description:To study the function of BAF250 during ES cell self renewal and differentiation Keywords: gene expression comparison between heterozygous,homozygoous and wild type ES cells
Project description:This experiment is to compared shTESK1 transduced induced pluripotent stem cells (iPSCs) with wild type embryonic stem cells (mES) and mouse embryonic fibroblasts (MEFs) in order to confirm that shTESK1 iPSCs are more close to ES-like state but not to their parental MEF cells. This ArrayExpress experiment includes data from two stable cell clones of shTESK1 transduced iPSCs. Microarray data for mES and MEFs have been archived in ArrayExpress under accession number E-MTAB-1188 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1188/).
Project description:Embryonic stem (ES) cells and embryos reversibly pause via chemical mTOR inhibition. In this study, we investigate the tissue-specific response to mTORi-induced pausing in ES and trophoblast stem (TS) cells. To resolve the sequential rewiring of the proteome, we conducted a time-series proteomics experiment at 1, 3, 6, 12, 24, and 48 hours upon induction of pausing, and at 1, 3, 6, 12, 24, and 48 hours upon release of pausing in ES and TS cells. We find that ES, but not TS cells pause reversibly. To optimise developmental pausing conditions, we reasoned that by understanding the difference in pausing response of ES and TS cells, we could identify which pathways are essential for pausing. We found that KEGG pathways related to amino acid degradation, fatty acid degradation, and DNA repair are upregulated in ES cells, but downregulated in TS cells during entry into pausing. Moreover, by targeted metabolomics, we found a depletion of short chain carnitines in the paused ES cells. To extend the length of developmental pausing, we supplemented paused embryos with L-carnitine. The L-carnitine supplementation facilitates lipid usage and prolongs the pausing length by 19 days through the establishment of a more dormant state.
Project description:This experiment is contains a subset of mouse organism part samples and RNA-seq data from experiment E-GEOD-39524 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39524/), which was originally submitted by the ENCODE consortium to NCBI Gene Expression Omnibus under accession number GSE39524 (http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE39524) and later imported to ArrayExpress as E-GEOD-39524.
Project description:Comparison among ES, EC, TS, NS, differentiated neural cells derived from NS and placenta in addition to ES-N2B27 neural induction. Keywords: cell type comparison design,development or differentiation design,time series design
Project description:Genome-wide chromatin state maps of murine embryonic stem (ES) cells, ES-derived neural progenitor cells and whole brain tissue. The data were generated to examine the correlation between histone and DNA methylation during lineage-commitment. Keywords: High-throughput ChIP-sequencing, Illumina, cell type comparison
Project description:Homozygous disruption of Bteb2/Klf5, a homolog of Drosophila gap gene Krüppel, led to increased expression of various differentiation marker genes, such as Fgf5, Cdx2, and Brachyury in mouse ES cells without compromising their ability to differentiate into all three germ layers. Upon removal of LIF, Klf5-deficient ES cells showed faster differentiation kinetics than wild-type ES cells. In contrast, overexpression of Klf5 in ES cells suppressed the transcription of differentiation marker genes, and maintained pluripotency in the absence of LIF. In order to search downstream genes of Klf5, we surveyed genes implicated in ES cell proliferation by microarray analysis Keywords: cell type comparison