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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome wide analysis of gene expression of rat ES cells, rat embryonic fibroblast cells and mouse ES cells

ABSTRACT: Rat ES cells were derived using 3I medium from E4.5 blastocysts. Rat embryonic fibroblast cells were derived form E14.5 embryos. To analyze the mechanism under the selfrenewal of rat ES cells, microarrays were used for the genome wide analysis of gene expressoin profiles in rat ES cells. Rat embryonic fibroblast cells and mouse ES cells were tested at same time as control. Our results from clustering analysis demonstrated that the gene expression profile of rat ES cells resembles mouse ES cells, but not REFs. Keyword: 3I medium; rat embryonic stem cells; mouse ES cells; rat embryonic fibroblast cells Rat ES cells were cultured in 3I medium; rat embryonic fibroblast cells were derived and cultured GMEM/10% FBS; mouse ES cells (C57/BL6)were cultured in GMEM/10% FBS added LIF and feeder cells were removed before RNA extraction. Three replicates each.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Ping Li

PROVIDER: E-GEOD-13681 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Germline competent embryonic stem cells derived from rat blastocysts.

Li Ping P Tong Chang C Mehrian-Shai Ruty R Jia Li L Wu Nancy N Yan Youzhen Y Maxson Robert E RE Schulze Eric N EN Song Houyan H Hsieh Chih-Lin CL Pera Martin F MF Ying Qi-Long QL

Cell 20081201 7

Rats have important advantages over mice as an experimental system for physiological and pharmacological investigations. The lack of rat embryonic stem (ES) cells has restricted the availability of transgenic technologies to create genetic models in this species. Here, we show that rat ES cells can be efficiently derived, propagated, and genetically manipulated in the presence of small molecules that specifically inhibit GSK3, MEK, and FGF receptor tyrosine kinases. These rat ES cells express pl ...[more]

PMID: 19109898

Similar Datasets

Genome wide analysis of gene expression of rat ES cells, rat embryonic fibroblast cells and mouse ES cells

Project description:Rat ES cells were derived using 3I medium from E4.5 blastocysts. Rat embryonic fibroblast cells were derived form E14.5 embryos. To analyze the mechanism under the selfrenewal of rat ES cells, microarrays were used for the genome wide analysis of gene expressoin profiles in rat ES cells. Rat embryonic fibroblast cells and mouse ES cells were tested at same time as control. Our results from clustering analysis demonstrated that the gene expression profile of rat ES cells resembles mouse ES cells, but not REFs. Keyword: 3I medium; rat embryonic stem cells; mouse ES cells; rat embryonic fibroblast cells

2008-11-25 | GSE13681 | GEO

Genome wide analysis of gene expression of rat ES cells, rat embryonic fibroblast cells and mouse ES cells

Project description:Genome wide analysis of gene expression of rat ES cells, rat embryonic fibroblast cells and mouse ES cells

| PRJNA110431 | ENA

Embryonic stem cells culture conditions support distinct ES cell states associated with specific developmental stages and cell types

Project description:Identification of transcripts in murine embryonic stem (ES) cell lines growing under 3 different self-renewing conditions; GMEM + 10% FCS, N2B27 + 2i (1 μM PD032 and 3 μM CHIR99021) and knockout serum replacement (KOSR) medium (80% Knockout DMEM, 20% Knockout Serum Replacement). Under all conditions, ES cells were grown on gelatin-coated dishes and passaged by trypsinisation. ES cells were cultured in each condition for at least 3 passages prior to sample collection. The aim of this array experiment is to identify significant differences in transcript levels of ES cells grown under different conditions. Differences of transcript levels from the different conditions should be consistent among the biological and technical replicates for each.

2016-07-14 | GSE72445 | GEO

Proteomics Identifies Differences in Fibrotic Potential of Exosomes from Human Tendon and Muscle Fibroblasts

Project description:Fibroblasts are the powerhouses responsible for the production and assembly of extracellular matrix. Their activity needs to be tightly controlled especially within the musculoskeletal system, where changes to extracellular matrix composition affect force transmission and mechanical loading that are required for effective movement of the body. Extracellular vesicles, including exosomes, are a mode of cell-cell communication within and between tissues, which has been largely characterised in cancer. However, it is unclear what the role of healthy fibroblast-derived extracellular vesicles is during tissue homeostasis. Here, we performed proteomic analysis of exosomes derived from primary human muscle and tendon cells to identify the potential functions of healthy fibroblast-derived exosomes. Mass spectrometry-based proteomics revealed comprehensive profiles for exosomes released from healthy human fibroblasts from different tissues. We found that fibroblast-derived exosomes were more similar than exosomes from differentiating myoblasts, but there were significant differences between tendon fibroblasts and muscle fibroblasts exosomes. Exosomes from tendon fibroblasts contain higher levels of proteins that support extracellular matrix synthesis, including TGFβ1, and muscle fibroblast exosomes contain a higher abundance of MMP2. Our data demonstrates a marked heterogeneity among healthy fibroblast-derived exosomes, indicating shared tasks between exosomes of skeletal muscle myoblasts and fibroblast, whereas tendon fibroblast exosomes has a marked fibrotic potential in human tendon tissue. These findings suggest an important role for exosomes in tissue homeostasis of both tendon and skeletal muscle in humans.

2021-09-09 | PXD018233 | Pride

Human embryonic stem cells

Project description:Undifferentiated human embryonic stem cells grown on mouse embryonic fibroblast feeder layers. HES3 and HES4 are proprietary human ES cell lines of ES Cell International Pte Ltd. Singapore. Keywords: other

2004-01-19 | GSE608 | GEO

GRO-seq in mouse Epiblast-primed, Primitive endoderm-primed, and differentiated endoderm cells

Project description:The identification of changes in transcriptional regulation during priming and differentiation of embryonic stem (ES) cells towards the endoderm lineage. Specific populations of ES cells, either primed or committed to endoderm, were isolated and subjected to global nuclear run on sequencing (GRO-Seq). The hHex-Venus (HV) reporter ES cell line, HVJu5.1 (Canham et al., 2010) was used to isolate HV- and HV+ ES cells. Primed ES cells were identified based on the expression of the HV marker in addition to the cell surface marker of undifferentiated ES cells, SSEA-1, (the lower and upper 25% of SSEA-1+, HV expressing cells). When challenged to differentiate, HV- ES cells are primed towards an epiblast fate, while HV+ ES cells are primed towards primitive endoderm. However, these populations are considered primed, rather than committed, as they will readily interconvert when re-introduced into standard ES cell culture conditions. ES cells were grown in self-renewing conditions (GMEM, LIF, 10% FCS, plated on gelatin coated dishes). Endoderm was obtained by differentiating ES cells in medium without the cytokine LIF for 5 days. The HV+, SSEA-1- differentiated fraction was then sorted and represents an early stage in endoderm differentiation.

2022-01-03 | GSE58503 | GEO

Gene expression study in skin fibroblasts

Project description:To investigate the in vivo developmental potential, we generated dedifferentiated-skin fibroblast from adult skin fibroblasts with a FVB background, a different genetic strain from the protein-donor embryonic stem (ES) cell. Primary cardiac fibroblast (cFB) was cultered from an adult C57/BL mouse to compare with ES cells(E14-mES, C57-mES). We also introduced C57 background ES cell-derived extract proteins into cFB by reversible permeabilisation. The ES-like cells (colonies) were expanded with subculture every 3 to 5 days using the standard ES cell culture protocol.

2018-11-01 | GSE21493 | GEO

Fgf and Esrrb integrate epigenetic and transcriptional networks that regulate self-renewal of Trophoblast Stem Cells

Project description:Esrrb is a transcription factor implicated in embryonic stem (ES) cell self-renewal, yet its knockout causes intrauterine lethality due to defects in trophoblast development. Here we show that in trophoblast stem (TS) cells, Esrrb is a downstream target of fibroblast growth factor (Fgf) signalling and is critical to drive TS cell self-renewal. In contrast to its occupancy of pluripotency-associated loci in ES cells, Esrrb sustains the stemness of TS cells by direct binding and regulation of TS cell-specific transcription factors including Elf5 and Eomes. To elucidate the mechanisms whereby Esrrb controls the expression of its targets, we characterized its TS cell-specific interactome by mass spectrometry. Unlike in ES cells, Esrrb interacts in TS cells with the histone demethylase Lsd1 and with the RNA Polymerase II-associated Integrator complex. Our findings provide new insights into both, the general and context-dependent wiring of transcription factor networks in stem cells by master transcription factors.

2015-07-24 | PXD002183 | Pride

Human embryonic stem cells

2004-01-18 | E-GEOD-608 | biostudies-arrayexpress

Undifferentiated mouse embryonic stem cells, differentiated nestin-positive cells and fibroblast feeder layer.

Project description:Embryonic stem (ES) cells and ES cell-derived progeny characterized by nestin expression (including neural progenitors) were studied (three independent experiments). The mouse ES cell line R1 was cultured on a feeder layer of mouse embryonic fibroblasts (FL). ES cells were differentiated into nestin-positive cells for 4+8 days and 4+11 days according to the differentiation protocol by Rolletschek et al. (Mechanisms of Development 105, 93-104, 2001). The study was performed with three independent cell cultures (= triplicates). RNA was prepared from both undifferentiated ES cells and ES cell-derived nestin-positive cells, and from fibroblast feeder cells. Keywords = ES cell Keywords = nestin positive cells Keywords = feeder layer Keywords: other

2005-09-17 | GSE2375 | GEO

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