ESCs_172-1_LIF_tR_comparison
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Vaggelis Harokopos
PROVIDER: E-MEXP-3012 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We measured genome-wide gene expression of embryonic stem cells derived from eight genetically diverse inbred mouse strains. We derived and cultured cells in LIF+2i media with feeders, and removed feeders prior to RNA collection. All lines were passage 6-8 when RNA was collected. We collected RNA from three biological replicate cell lines derived from each of the eight inbred mouse strains. For three strains (C57BL/6J, NOD, and PWD/PhJ), we obtained technical replicate RNA-Seq runs of each of the three biological replicate cell lines.
2020-08-13 | E-MTAB-7730 | biostudies-arrayexpress
Project description:RNA-binding proteins (RBPs) have essential roles in RNA-mediated gene regulation, and yet annotation of RBPs is limited mainly to those with known RNA-binding domains. To systematically identify the RBPs of embryonic stem cells (ESCs), we here employ interactome capture, which combines UV cross-linking of RBP to RNA in living cells, oligo(dT) capture and MS. From mouse ESCs (mESCs), we have defined 555 proteins constituting the mESC mRNA interactome, including 283 proteins not previously annotated as RBPs. Of these, 68 new RBP candidates are highly expressed in ESCs compared to differentiated cells, implicating a role in stem-cell physiology. Two well-known E3 ubiquitin ligases, Trim25 (also called Efp) and Trim71 (also called Lin41), are validated as RBPs, revealing a potential link between RNA biology and protein-modification pathways. Our study confirms and expands the atlas of RBPs, providing a useful resource for the study of the RNA-RBP network in stem cells.
2018-08-29 | PXD008914 | Pride
Project description:SET-domain containing proteins play a vital role in regulating gene expression during development through modifications in chromatin structure. To study molecular function of SET domain containing 5 (Setd5), we assessed global changes in the mouse embryonic stem cell transcriptome when Setd5 gene is knocked out.
2016-12-13 | E-MTAB-5189 | biostudies-arrayexpress
Project description:Schizophrenia is a severe and debilitating neuropsychiatric disorder with the involvement of genetic and environmental factors contributing to its pathogenesis. The specific role of the brain cell types in the disease remains uncovered due to the difficulties in accessing diseased tissue. This study analysed molecular alterations in human induced pluripotent stem cells derived from fibroblasts from control subject and individual with schizophrenia and further differentiated to neuron to identify genes relevant for the development of schizophrenia. We identified 228 genes that are involved with metabolic processes, signal transduction, nervous system development, regulation of neurogenesis and neuronal differentiation. These genes were analysed in expression microarrays of post-mortem brain tissue (frontal cortex) of additional patients with schizophrenia and normal individuals revealing only six common genes: CACNA1E, CEBPB, DUX4, EDNRA, SPHK1 and SPRY4. Furthermore, a co-expression network analysis of the 228 genes revealed a non-conserved module enriched for genes associated with oxidative stress and negative regulation of cell differentiation as involved with schizophrenia. This study supports the relevance of using cellular approaches to dissect molecular aspects of neurogenesis with impact in the schizophrenic brain. Biopsies of primary human fibroblasts from a 48-year-old woman with DSM-IVTR schizophrenia defined as treatment-resistant under clozapine treatment (SZCP) were collected in parallel with a control subject (CON) negative for any major lifetime DSM-IVTR diagnosis. Fibroblasts underwent primary culture procedures to generate hiPSCs and were subsequently differentiated into neurons (NPC). Samples generation and culture conditions are described in Paulsen et al. (2011). Five replicates of expression microarray experiments using a reference design, where test sample (NPC) is derived from reference sample (hiPSC).
2014-10-09 | E-GEOD-62105 | biostudies-arrayexpress
Project description:RNA-seq of Ronin/Thap11 knockout and heterozygous control mouse ES cells to assess the role of Ronin
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Project description:The associated files are mass spec data from size exclusion chromatographic separations of mouse embryonic stem cells with and without RNAse A treatment.
2019-10-18 | PXD014607 | Pride
Project description:We differentiated mouse embryonic stem (mES) cells spontaneously into embryoid bodies (EBs). Gene expression of biological replicates of undifferentiated ES cells (0-day), 4-day, 8-day and 14-day EBs were measured by Affymetrix microarrays. Keywords: time course Mouse embroynic stem cells were spontaneously into EBs. The gene expression was measured on undifferentiated mES cells on gelatin (0-day), undifferentiated mES cells sorted by FACS on Oct4 GFP-day (0-day), 4-day, 8-day and 14-day EBs.
2010-03-09 | E-GEOD-12550 | biostudies-arrayexpress
Project description:We have been able to derive EpiSC-like pESC lines from in vivo produced porcine blastocysts. Our cell lines showed AP activity, expressions of the genes Oct4, Sox2, Nanog, Rex1, TDGF1, bFGF, FGFR1, FGFR2, Nodal and Activin-A involved in pluripotency and signaling pathways and in vitro differentiation potential, displaying similarities to epiblast stem cells or hES cells. Porcine blastocysts were cultured on mitotically inactivated mouse embryonic fibroblasts (MEFs) in pESC medium. Following 5-7 days of culture, we observed EpiSC-like primary colonies derived from day 7 in vivo-produced. These EpiSC-like pESC colonies were mechanically dissociated into several clumps using pulled glass pipettes 10-15 days after seeding. Dissociated clumps were then re-seeded on fresh MEFs, and subsequent EpiSC-like pESC lines were routinely passaged via the pulled glass pipette method every 5-7 days. Our cell lines maintained stemness and a stable morphology for more than 56 passages. The main purpose of the present study was to investigate gloval gene expression from porcine embryonic stem cells.
2011-12-31 | E-GEOD-32506 | biostudies-arrayexpress
Project description:Compare a single sample run with two different technologies: Illumina 450k methylation array and MIRA on NimbleGen This data is being published as a technical test of utility for a novel integrative genomic algorithm (COHCAP) Keywords: HES-2
2013-06-08 | E-GEOD-42707 | biostudies-arrayexpress
Project description:Parthenogenetic embryonic stem cells (PESCs) may have future utility in cell replacement therapies. We examined genome-wide mRNA expression profiles of monkey PESCs relative to ESCs derived from fertilized embryos. Several known paternally-imprinted genes were in the highly down-regulated group in PESCs compared to ESCs. Allele specific expression analysis of paternally-imprinted genes, i.e., those genes whose expression is down-regulated in PESCs, led to the identification of one novel candidate that was exclusively expressed from a paternal allele. Our findings suggest that PESCs could be used as a model for studying genomic imprinting and in the discovery of novel imprinted genes. Keywords: gene expression The transcriptomes of rhesus monkey embryonic stem cell lines derived from IVF-produced embryos (Oregon Rhesus Macaque Embryonic Stem, ORMES-22) were compared with rhesus monkey parthenogenetic embryonic stem cell lines (heterozygous rhesus Parthenogenetic embryonic stem cell lines, rPESC-2) and homozygous rhesus Parthenogenetic embryonic stem cell lines, ORMES-9). Moreover, the transcriptomes of rPESC-2 line were also compared with ORMES-9. Finally, the adult somatic skin fibroblasts were analyzed. Three biological replicates of each cell line (A, B, C) were analyzed.
2010-07-07 | E-GEOD-17964 | biostudies-arrayexpress