Effect of Pnpla6 gene silencing in D3 mouse embryonic stem cells
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE33974 | GEO | 2013/11/04
SECONDARY ACCESSION(S): PRJNA150509
REPOSITORIES: GEO
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Project description:Pnpla6 gene was silenced in D3 mouse embryonic stem cells and the cells were allowed to spontaneously differentiate. Transcription of the whole genome was analyzed 96 days afterwards and compared against control cells differentiated during the same time without previous silencing. Comparimg two experimental conditions: control differentiated cells versus Pnpla6 silenced differentiated cells.
2013-11-04 | E-GEOD-33974 | biostudies-arrayexpress
Project description:Increasing evidence provide support that the mammalian liver contains stem/progenitor cells, but their molecular phenotype, embryological derivation, cell biology as well as of their role in the liver cell turnover and regeneration remain to be further clarified. We report the isolation, characterization and reproducible establishment in line of a resident liver stem cell (RLSC) with immunophenotype and differentiative potential distinct from other previously reported liver precursor/stem cells. RLSCs, derived from foetal and neonatal murine livers as well as from immortalized hepatocytic MMH lines and established in lines, are Sca+, CD34-, CD45-, alfa-fetoprotein+, albumin-. This immunophenotype suggests a non-haematopoietic origin. RLSCs transcriptional profile, defined by microArray technology, highlighted the expression of a broad spectrum of âplasticity-related genesâ and âdevelopmental genesâ suggesting a multi-differentiative potential. RLSCs, indeed, spontaneously differentiate into hepatocytes and cholangiocytes and, when cultured in appropriate conditions, into mesenchymal and neuro-ectodermal cell lineages, such as osteoblasts/osteocytes, chondrocytes, astrocytes and neuronal cells. RLSCs capability to spontaneously differentiate into hepatocytes, the lack of albumin expression and the broad differentiative potentiality locate them in a pre-hepatoblast/liver precursor cells hierarchical position. In conclusion, RLSCs may provide an useful tool to improve liver stem cell knowledge and to assess new therapeutic approaches for liver diseases. Experiment Overall Design: We compared the gene expression profile of a RLSC line to that of the previously characterised hepatocytic differentiated cell line MMH-D3 (ref Amicone), using Affymetrix Mouse430_2 GeneChip array.
2008-06-18 | E-GEOD-7038 | biostudies-arrayexpress
Project description:Increasing evidence provide support that the mammalian liver contains stem/progenitor cells, but their molecular phenotype, embryological derivation, cell biology as well as of their role in the liver cell turnover and regeneration remain to be further clarified. We report the isolation, characterization and reproducible establishment in line of a resident liver stem cell (RLSC) with immunophenotype and differentiative potential distinct from other previously reported liver precursor/stem cells. RLSCs, derived from foetal and neonatal murine livers as well as from immortalized hepatocytic MMH lines and established in lines, are Sca+, CD34-, CD45-, alfa-fetoprotein+, albumin-. This immunophenotype suggests a non-haematopoietic origin. RLSCs transcriptional profile, defined by microArray technology, highlighted the expression of a broad spectrum of “plasticity-related genes” and “developmental genes” suggesting a multi-differentiative potential. RLSCs, indeed, spontaneously differentiate into hepatocytes and cholangiocytes and, when cultured in appropriate conditions, into mesenchymal and neuro-ectodermal cell lineages, such as osteoblasts/osteocytes, chondrocytes, astrocytes and neuronal cells. RLSCs capability to spontaneously differentiate into hepatocytes, the lack of albumin expression and the broad differentiative potentiality locate them in a pre-hepatoblast/liver precursor cells hierarchical position. In conclusion, RLSCs may provide an useful tool to improve liver stem cell knowledge and to assess new therapeutic approaches for liver diseases. Keywords: cell type comparison
2008-06-03 | GSE7038 | GEO
Project description:Pediococcus acidilactici D3 strain:D3 Genome sequencing and assembly
| PRJNA193440 | ENA
Project description:Williamsia sp. D3 strain:D3 Genome sequencing and assembly
| PRJNA228956 | ENA
Project description:The c-Myb transcription factor is highly expressed in immature hematopoietic cells and down-regulated during differentiation. To define the role of c-Myb during the terminal differentiation of hematopoietic precursors, we studied the effects of its silencing in human primary CD14-myeloblasts, which maintain a granulo-monocyte differentiation bipotentiality. c-Myb-silenced myeloblasts were blocked in the G1 phase of the cell cycle at 24 hours post-nucleofection and subsequently were forced towards macrophage differentiation, as demonstrated by immunophenotypic and morphological analysis. Indeed, c-Myb-silenced CD14- cells differentiate to macrophage even after the treatment with ATRA 10-6 M, demonstrating that the c-Myb knockdown strongly impairs the ability of myeloblasts to differentiate to granulocytes. Gene expression profiling of c-Myb-silenced CD14- cells identified some potential c-Myb targets that can account for these effects.
2010-07-14 | GSE21943 | GEO
Project description:BACKGROUND & AIMS- More frequent interaction of bacteria with the colonic epithelium is associated with ulcerative colitis (UC). The identities of all proteins which promote bacterial clearance in colonic epithelial cells are unknown. Previously, we discovered that dCAP-D3 (Chromosome Associated Protein-D3), regulates responses to bacterial infection. We examined whether CAP-D3 promotes bacterial clearance in human colonic epithelium. METHODS- Clearance of Salmonella or adherent-invasive Escherichia coli LF82 was assessed by gentamycin protection assays in HT-29 and Caco-2 cells expressing CAP-D3 shRNA. CAP-D3 levels in colonic epithelial cells from healthy and UC patient tissues were analyzed by immunoblot. RNA-sequencing identified bacterially-induced CAP-D3 target genes. The role of CAP-D3 target genes in bacterial clearance was analyzed by gentamycin protection assays, immunofluorescent staining, and by using pharmacologic inhibitors. RESULTS- CAP-D3 expression was reduced in colonic epithelial cells from UC patients with active disease. Reduction of CAP-D3 expression inhibited autophagy and decreased intracellular bacterial clearance. The components of the heterodimeric SLC7A5/SLC3A2 amino acid transporter were identified as CAP-D3 target genes; their levels increased in infected, CAP-D3 deficient cell lines and in cells from UC patients. In HT-29 cells, this resulted in earlier SLC7A5 recruitment to Salmonella-containing vacuoles, increased mTOR activity, and enhanced bacterial survival. Inhibition of SLC7A5/SLC3A2 or mTOR activity rescued the bacterial clearance defect in CAP-D3 deficient cells. CONCLUSIONS- CAP-D3 attenuates amino acid transporter transcription to promote bacterial autophagy in colon epithelial cells. CAP-D3 protein levels are decreased in patients with active UC, suggesting that CAP-D3 is a potential therapeutic target to restore mucosal homeostasis in UC patients.
2015-09-15 | GSE62520 | GEO
Project description:Simulium sp. D3-Man isolate:D3-Man Genome sequencing
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Project description:In humans, vitamin D3 is a secosteroid, a prohormonal precursor of biologically active hydroxyforms. Vitamin D3 is related to periodontitis. The third American Health and Nutrition Survey found that plasma 25(OH)D3 levels are negatively correlated with attachment loss in people aged >50 years. The relationship between vitamin D3 and periodontitis remains to be investigated. We sent human gingival fibroblasts treated by vitamin D3 for transcriptome sequencing.
2022-09-09 | GSE212728 | GEO
Project description:We have carried out global gene expression analysis to clarify the interrelationship between 1,25-dihydroxyvitamin D3 and differentiation-driven gene expression patterns in developing human monocyte-derived dendritic cells. Monocytes were treated with 10 nM 1,25-dihydroxyvitamin D3 or vehicle 14 hours after plating for 12 hours or 5 days. Monocytes, differentiating dendritic cells (+/-1,25-dihydroxyvitamin D3 for 12 hours) and immature dendritic cells (+/-1,25-dihydroxyvitamin D3 for 5 days) were harvested. This design allows one to identify genes regulated by differentiation and/or 1,25-dihydroxyvitamin D3 in human monocyte-derived dendritic cells.
2009-02-15 | GSE13762 | GEO