Gene microarray screening of RNA from bruce 4 ES cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE29926 | GEO | 2011/06/14
SECONDARY ACCESSION(S): PRJNA140865
REPOSITORIES: GEO
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Project description:The sample is wild type male bruce 4 ES cells which has been used in core f to generate knockout mice. RNA samples from wild type male bruce 4 ES cells, which has been used in core f to generate knockout mice, were screened. Scraped cells, pre-plated and non-pre-plated trypsinized cells were compared to determine the effects of trypsin and fibroblasts on gene expression of the ES cells. Mouse ES cell pellets were delivered to Core E for RNA Extraction. *Concurrent analysis of glycan profiles in these cells was performed in Core C*. RNA from scraped ES cells, trypsinized cells, and pre-plated trypsinized cells was isolated and prepared in triplicate. RNA was labeled and hybridized to the GLYCOv3 array. Resulting Gene expression patterns were analyzed by Core F.
2011-06-14 | E-GEOD-29926 | biostudies-arrayexpress
Project description:Core circuits of transcription factors stabilize stem and progenitor cells by suppressing genes required for differentiation. We do not know how such core circuits are reorganized during cell fate transitions to allow differentiation and lineage choice to proceed. Here, we asked how the pluripotency circuit, a core transcriptional circuit that maintains mouse embryonic stem (ES) cells in a pluripotent state, is dismantled as ES cells differentiate and choose between the neural ectodermal and mesendodermal progenitor cell fates. When ES cells are recultured from pluripotency maintaining conditions to the basal media N2B27, the expression of the pluripotency circuit genes begins to change. At 48 hours post N2B27 addition, the ES cells are competent to respond to differentiation signals. Here, our microarray analysis compares the gene expression profile of ES cells vs. the gene expression profile of cells that have been treated with N2B27 for 48 hours, reaching the competent state.
2011-05-03 | GSE29005 | GEO
Project description:Core circuits of transcription factors stabilize stem and progenitor cells by suppressing genes required for differentiation. We do not know how such core circuits are reorganized during cell fate transitions to allow differentiation and lineage choice to proceed. Here, we asked how the pluripotency circuit, a core transcriptional circuit that maintains mouse embryonic stem (ES) cells in a pluripotent state, is dismantled as ES cells differentiate and choose between the neural ectodermal and mesendodermal progenitor cell fates. When ES cells are recultured from pluripotency maintaining conditions to the basal media N2B27, the expression of the pluripotency circuit genes begins to change. At 48 hours post N2B27 addition, the ES cells are competent to respond to differentiation signals. Here, our microarray analysis compares the gene expression profile of ES cells vs. the gene expression profile of cells that have been treated with N2B27 for 48 hours, reaching the competent state. 2 x mouse ES cells in pluripotency maintaining conditions. 3 x mouse ES cells after 48 hr of N2B27 culture
2011-05-03 | E-GEOD-29005 | biostudies-arrayexpress
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
Project description:TG-interacting factor1 (Tgif1) is well-known as a transcriptional repressor in transforming growth factor beta (TGFβ) signaling pathway. Target mapping of ES cell core factors in mouse embryonic stem (ES) cells revealed that Tgif1 is occupied by Oct4 and Nanog. Moreover, recent interactome study of mouse gene regulatory regions showed a preferential regulation of Tgif1 by mouse ES cell specific enhancers. However, the detailed role and mode of actions of Tgif1 in stem cell maintenance and development remains elusive. We show that Tgif1 is indispensable for self-renewal and pluripotency of mouse embryonic stem (ES) cells. Aberrant expression of Tgif1 promotes differentiation of ES cells even in the presence of LIF in part by deregulation of pluripotency factors. Intriguingly, we find that Tgif1 level is a critical factor to determine specific lineage commitment in a dosage-dependent manner. We further show that Tgif1 interacts with ES cell core factors and co-localizes at their binding sites, which eventually restricts expression of ES cell core factors including Oct4, Sox2, and Nanog. Taken together, we provide new insights into the roles of Tgif1 in maintenance as well as differentiation of ES cells.
2015-09-26 | GSE55404 | GEO
Project description:Borrelia anserina Es strain:Es Genome sequencing
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Project description:Gene expression as measured by microarray, in order to determine the cohort of differentially expressed genes, in each of two different mutant ES cell lines (Cbx1 and Jarid2), each comparing the respective null mutant ES cells to revertant (single allele expression) mutant ES cells. Hybridization was performed concurrently. Experiments are: 1) Cbx1 null mutant (Cbx1^tm1a(EUCOMM)Wtsi/Cbx1^tm1Wcs) compared to revertant mutant (Cbx1^tm1c(EUCOMM)Wtsi/Cbx1^tm1Wcs) ES cell lines (n=6 per genotype). 2) Jarid2 null mutant (Jarid2^tm1a(KOMP)Wtsi/Jarid2tm1Wcs) compared to revertant mutant (Jarid2^tm1c(KOMP)Wtsi/Jarid2tm1Wcs) ES cell lines (n=3 per genotype). Biological replicates (individual ES clones) were used. Parental ES cell lines are from the International Knockout Mouse Consortium (IKMC - EUCOMM and KOMP-CSD programmes) and were modified to generate null ES cells using bi-allelic gene targeting with a targeted trapping vector generated by re-purposing Intermediate Vectors from the IKMC resource. Revertant ES cell lines were generated by using Flp recombinase to revert the IKMC tm1a null allele to the conditional tm1c allele, in order to reinstate gene expression from one allele. The tm1Wcs allele is constitutive null.
2017-09-12 | E-MTAB-5930 | biostudies-arrayexpress
Project description:Transcriptional profiling of mouse embryonic stem cells comparing control untreated ES cells with Zscan5b knockout ES cells
2018-12-27 | GSE124354 | GEO
Project description:Mouse embryonic stem cells lines derived from different mouse strains show considerable variation concerning their culture conditions, gene targeting efficiency and germ line transmission capacity. To gain insight into the basis for this phenomenon, we generated a SAGE library of the C57BL/6 derived ES cell line Bruce-4 and compared their gene expression to 129 strain-derived cells, which in general show the best performance in gene targeting experiments. Gene Ontology (GO) analyses for functional groups of genes demonstrated considerably higher expression of clusters indicating cellular differentiation as well as cell-cell and cell-matrix adhesion in R1 than in Bruce-4 cells. At the single gene level, almost 90% of the most strongly expressed transcripts in each library were significantly differential. Regarding transcripts that have been linked to stem cell state, seven of the 20 selected genes were expressed in both cell lines, eleven showed stronger expression in Bruce-4 ES cells and only one in R1 cells. These results suggest that expression of “stemness” genes cannot be used as a sole criterion for efficiency of ES cells in gene targeting experiments. Keywords: Embryonic stem cells, SAGE, gene expression profile We generated a SAGE library of the C57BL/6-derived ES cell line Bruce-4 and compared their gene expression to an already available SAGE library of 129-derived R1 ES cells generated by Anisimov et al (GSM72878).
2007-09-21 | E-GEOD-9078 | biostudies-arrayexpress
Project description:Mouse embryonic stem cells lines derived from different mouse strains show considerable variation concerning their culture conditions, gene targeting efficiency and germ line transmission capacity. To gain insight into the basis for this phenomenon, we generated a SAGE library of the C57BL/6 derived ES cell line Bruce-4 and compared their gene expression to 129 strain-derived cells, which in general show the best performance in gene targeting experiments. Gene Ontology (GO) analyses for functional groups of genes demonstrated considerably higher expression of clusters indicating cellular differentiation as well as cell-cell and cell-matrix adhesion in R1 than in Bruce-4 cells. At the single gene level, almost 90% of the most strongly expressed transcripts in each library were significantly differential. Regarding transcripts that have been linked to stem cell state, seven of the 20 selected genes were expressed in both cell lines, eleven showed stronger expression in Bruce-4 ES cells and only one in R1 cells. These results suggest that expression of “stemness” genes cannot be used as a sole criterion for efficiency of ES cells in gene targeting experiments. Keywords: Embryonic stem cells, SAGE, gene expression profile
2007-09-22 | GSE9078 | GEO