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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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A Notch ligand, Delta-like 1 functions as an adhesion molecule for mast cells

ABSTRACT: To assess the effect of over-expression of Delta-like 1 on OP9 cells on gene expression in terms of Notch signaling and adhesion molecules, gene expressions of OP9, OP9-GFP (carrying GFP gene) and OP9-DL1 (carrying GFP and DL1 gene) cells (Immunity 2002;17:749-756) were analyzed. Gene expression of OP9, OP9-GFP and OP9-DL1 were compared.

ORGANISM(S): Mus musculus

SUBMITTER: Akihiko Murata

PROVIDER: E-GEOD-22659 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A Notch ligand, Delta-like 1 functions as an adhesion molecule for mast cells

Project description:To assess the effect of over-expression of Delta-like 1 on OP9 cells on gene expression in terms of Notch signaling and adhesion molecules, gene expressions of OP9, OP9-GFP (carrying GFP gene) and OP9-DL1 (carrying GFP and DL1 gene) cells (Immunity 2002;17:749-756) were analyzed.

2010-10-01 | GSE22659 | GEO

Murine CD8+ T cells: in vitro-derived vs. thymocytes

Project description:Transcriptional profiling of mouse in-vitro derived CD8+ cells (obtained after culturing BM-HSCs isolated from B6 mice) with OP9-DL1 cells for 35 days were compared to CD8+ thymocytes isolated from 4-5 weeks old B6 mice. Our goal was to determine similarities and differences in gene expression profile between in vitro-derived CD8+ cells and CD8+ cells isolated from the thymus. The procedure of in vitro differentiation of HSC using OP9-DL1 cocultures was previously described by: Schmitt, T. M., and J. C. Zuniga-Pflucker. 2002. Induction of T cell development from hematopoietic progenitor cells by delta-like-1 in vitro. Immunity 17:749-756 and Holmes, R., and J. C. Zuniga-Pflucker. 2009. The OP9-DL1 system: generation of T-lymphocytes from embryonic or hematopoietic stem cells in vitro. Cold Spring Harb Protoc 2009:pdb prot5156.

2012-09-05 | GSE37669 | GEO

Murine CD8+ T cells: in vitro-derived vs. thymocytes

2012-09-05 | E-GEOD-37669 | biostudies-arrayexpress

Gene expression profiles in human ESCs and ESC-derived purified cardiomyocytes

Project description:Differences of metabolism-related gene expression profiles in human ESCs and ESC-derived purified cardiomyocytes were analyzed and successfully identified. Human ESCs and ESC-derived purified cardiomyocytes were used for this experiment.

2016-03-31 | E-GEOD-77518 | biostudies-arrayexpress

Acetylated Histone Reader Brd4 functions as Repair Adaptor in Immunoglobulin Class Switch Recombination

Project description:Class Switch Recombination (CSR) is a B cell specific genomic alteration induced by activation induced cytidine deaminase (AID)-dependent DNA break, followed by repair and recombination at the immunoglobulin heavy-chain locus. The involvement of several chromatin-associated factors in promoting AID-induced DNA break formation has been reported. However, the involvement of chromatin adaptors at the repair phase of CSR remains unknown. Here, we provide evidence that acetylated histone reader Brd4 is critical to the repair and recombination step of CSR. Brd4 was recruited to the AID-induced DNA break region, and depletion of Brd4 from the S region chromatin by knockdown or a chemical inhibitor JQ1 causes CSR impairment without affecting AID-induced DNA break generation. Such inhibition of Brd4 suppressed the accumulation of 53BP1 and UNG at the cleaved S regions, perturbed switch donor-switch acceptor microhomology length and reduced Igh/c-myc translocation. We conclude that Brd4 serves as a histone-reader platform required for the recruitment of CSR repair components. Brd4 were depleted from the chromatin by either siRNA treatment or JQ1 (40nM) addition in CH12F3-2A cells in the presence of CIT stimulation. RNA from each samples were extracted and relative difference in transcript level were compared with control RNAi- and DMSO-treated, CIT-stimulated samples.

2014-06-20 | E-GEOD-52239 | biostudies-arrayexpress

Lhx2-regulated genes in hematopoietic stem cell (HSC)-like cells differentiated from mouse embryonic stem (ES) cells

Project description:We previously demonstrated that hematopoietic stem cell (HSC)-like cells are robustly expanded from mouse embryonic stem (ES) cells by enforced expression of Lhx2, a LIM-homeobox domain (LIM-HD) transcription factor. Here we established an ES cell line which conditionally expressed Lhx2 by Tet-On system. The ES cells were differentiated into HSC-like cells by Lhx2 expression. Lhx2-regulated genes were identified by comparing the HSC-like cells with those cultured in the absence of Lhx2 expression. Mouse ES with inducible Lhx2 were differentiated on OP9 stromal cells into hematopoietic lineage. On day 5 of the differentiation induction,Lhx2 expression was started by the addition of doxycycline (dox) and the cells were cultured on OP9 stromal cells in the presence of IL-6 and SCF. On day 20, HSC-like cells were harvested and re-seeded onto OP9 stromal cells in the absence of Lhx2 expression by dox-removal for 3 days. these cells were compared with the original HSC-like cells.

2013-08-26 | E-GEOD-44778 | biostudies-arrayexpress

Tracing the conversion process for primordial germ cells to pluripotent stem cells

Project description:The overall gene expression profiles revealed by this system provide novel insight into how pluripotency is acquired in germ-committed cells. In the study presented here, we employed FACS sorting to purify pluripotent candidate cells during the culture period

2012-04-24 | E-GEOD-37261 | biostudies-arrayexpress

Gene expression profiling of endothelial cells derived from Foxo1(+/+) and Foxo1(-/-) ES cells in response to VEGF

Project description:VEGF induces elongation of endothelial cells (ECs) that are derived from wild-type (Foxo1(+/+)) ES cells. VEGF-induced EC elongation is an important process of angiogenesis. ECs derived from Foxo1(-/-) ES cells fail to elongate in response to VEGF. Gene expression profiling of wild-type and Foxo1(-/-) ECs in the presence or absence of VEGF stimulation identifies responsible genes that regulate EC elongation. One wild-type (Foxo1(+/+)) ES cell clone and one Foxo1(-/-) ES cell clone were used. ES cells were cultured on OP9 stromal cell layer in the presence or absence of VEGF (10 ng/ml). After 6.5 days, VE-cadherin+ CD31+ ECs were isolated by FACS and used for total RNA extraction. Three independent experiments were performed for each condition.

2016-02-16 | E-GEOD-76366 | biostudies-arrayexpress

Identification of a novel NF-kB target gene in human triple-negative breast cancer cells

Project description:Analysis of human triple-negative breast cancer cells (TNBCs) which have high NF-kB activity. Proteins derived from NF-ÎºB target genes might be molecular targets for cancer therapy. Results provide new insights into tumor proliferation mechanisms. Exp. 1: Mock MDA-MB-436 cells vs. MDA-MB-436 cells infected with Adenovirus-IkBaSR; Exp. 2: MDA-MB-436 cells infected with Adenovirus-GFP vs. MDA-MB-436 cells infected with Adenovirus-IkBaSR.

2015-02-20 | E-GEOD-56812 | biostudies-arrayexpress

The change of mRNA expression in murine immortalized podocyte after miR-26a silencing

Project description:The change of mRNA expression in murine immortalized podocyte were analyzed after miR-26a silencing. These results provide a basical information of molecular pathology in podocyte biology. Mouse podocytes immortalized by temperature sensitive SV40 were used. Podocyte cultures grown at 33 °C were trypsinized and then cultured with RPMI-1640 without antibiotics in 24-well plates at 60–70% confluence for 2 days. On day 3, an anti-miR negative control (40 pmol) or the miR-26a miRNA inhibitor (40 pmol) was transfected to podocytes. The cells were analyzed after culturing for 24 hour.

2014-10-01 | E-GEOD-51210 | biostudies-arrayexpress

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