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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of mouse B16-F10 melanoma cells stimulated with TIM-3

ABSTRACT: The effect of TIM-3 stimulation was studied on B16F10 mouse melanoma cells, in vitro. Experiment Overall Design: Cy3: B16F10 mouse melanoma cells, treated by unspecific goat IgG (control) for 2 hours. Experiment Overall Design: Cy5: B16F10 mouse melanoma cells, in vitro, treated by an agonist goat polyclonal anti-mouse TIM3 antibody (RnD Systems) for 2 hours. Experiment Overall Design: Four biological replicates were used (in this study, biological replicate means different passage numbers of the same cell line). In each case, the treated sample (Cy5) was compared to its control one (Cy3) in Agilent dual-color microarray experiments.

ORGANISM(S): Mus musculus

SUBMITTER: Zoltan Wiener

PROVIDER: E-GEOD-14418 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcription profiling of mouse IgE/antigen-activated mast cells stimulated with TIM-3

Project description:TIM-3 is known to be expressed on dendritic cells, monocytes, melanoma cells, mast cells and on activated Th1 cells. In activated Th1 cells, stimulating TIM-3 by one of its ligands, galectin-9, leads to apoptosis and thus it plays a central role in terminating Th1-type immune responses. Interestingly, in IgE/antigen-activated mast cells TIM-3 enhances the production of IL-13 and IL-4. To get a more complete picture about the gene expression changes induced by TIM-3 in mast cells, in vitro differentiated mouse immature mast cells were stimulated by an agonist anti-TIM-3 antibody and IgE-sensitized mouse immature mast cells were activated by antigen and an agonist anti-TIM-3 antibody for 2 or 16 hours (overnight). Experiment Overall Design: Bone marrow cells were differentiated in RPMI + 10% FCS + 5 ng/ml mouse IL-3 + 40 ng/ml mouse SCF for >4 weeks. The purity of the cell cultures was >90% at this time point (FcERIa+/c-kit+ cells). These in vitro-differentiated immature mast cells were then treated by either control goat IgG or an agonist anti-mouse TIM-3 antibody (RnD Systems, 15 ug/ml for 2 or 16 hours). For the IgE/antigen-activated mouse mast cells, these in vitro-differentiated immature mast cells were sensitized by 5 ug/ml anti-DNP IgE (Sigma) for 1 hour and then treated with 100 ng/ml DNP-HSA (antigen, Sigma) and either control goat IgG or an agonist anti-mouse TIM-3 antibody (RnD Systems, 15 ug/ml) for 2 or 16 hours. The anti-TIM-3 samples were labeled by Cy5 and they were compared to the Cy3-labeled, goat IgG controls in a dual-color, paired experimental setup. The Agilent Whole Mouse Genome 4x44K expression microarray kit and Dual-Color Protocol version 5.5 were used in the experiments.

2009-10-15 | E-GEOD-14438 | biostudies-arrayexpress

PITX1 suppresses TERT transcription

Project description:Using microcell-mediated chromosome transfer (MMCT) into the mouse melanoma cell line, B16F10, we have previously found that human chromosome 5 carries a gene, or genes, that can negatively regulate TERT expression. To identify the gene responsible for the regulation of TERT transcription, we performed cDNA microarray analysis using parental B16F10 cells, telomerase negative B16F10 microcell hybrids with a human chromosome 5 (B16F10MH5), and its revertant clones (MH5R) with reactivated telomerase. Here we report the identification of PITX1, whose restoration leads to the downregulation of mouse tert (mtert) transcription, as a TERT suppressor gene. Additionally, both human TERT (hTERT) and mouse TERT (mtert) promoter activity can be suppressed by PITX1. We showed that three and one binding sites, respectively, within the hTERT and mtert promoters that express a unique conserved region are responsible for the transcriptional activation of TERT. Furthermore, we showed that PITX1 binds to the TERT promoter both in vitro and in vivo. Thus, PITX1 suppresses TERT transcription through direct binding to the TERT promoter, which ultimately regulates telomerase activity. We transferred intact human chromosome 5 into mouse melanoma B16F10 cells by microcell fusion. The microcell hybrids (MH5) exhibited suppression of telomerase, we also obtained revertant clones (MH5R) in which telomerase is reactivated. To identify the differentially expressed genes on human chromosome 5, we performed expression microarray analysis using these two clones and parental B16F10 cells.

2010-09-10 | E-GEOD-23216 | biostudies-arrayexpress

Adult_mouse_testis_CREM_ChIP_chip

Project description:Germ cells from adult mouse testes were isolated and ChIPed by CREM antibody. The purpose is to identify potential CREM targets during spermatogenesis. The CREM antibody ChIPed DNA segments were labeled with Cy5 and goat IgG ChIPed segments were labeled with Cy3 as control. No duplicates were designed.

2010-10-13 | E-GEOD-24623 | biostudies-arrayexpress

Expression Data from PECAM1+ and PECAM1- B16F10 Clones

Project description:We have isolated cells from the B16F10 melanoma cell line which express the vascular-selective marker PECAM1 Here we used microarrays to determine expression profile differences across the mouse genome to determine whether these cells display additional endothelial characteristics PECAM1+ and PECAM1- B16F10 clones, along with mouse endothelial cells were cultured and harvested for RNA, which was then used in an Affymetrix Mouse Gene 1.0 ST array to determine expression signatures

2014-07-19 | E-GEOD-59564 | biostudies-arrayexpress

The effect of TIM-3 stimulation on the gene expression profile of B16-F10 melanoma cells

Project description:The effect of TIM-3 stimulation was studied on B16F10 mouse melanoma cells, in vitro.

2009-10-01 | GSE14418 | GEO

Analysis of transcriptome of mouse melanoma cells co-cultured with HEK293T cells expressing mouse Siglec1.

Project description:To evaluate the effect of mouse Siglec1 on B16F10 melanoma we used co-culture methos where HEK293T cells were transiently transfected with plasmid containg mouse Siglec1 or empty plasmid (mock). These HEK293T cells were cultured with B16F10-GFP mouse melanoma cells for 18 hours in low binding plates. After 18 hours of incubation on 37°C, 5% CO2, melanoma cells were FACS sorted based on GFP expression and total RNA was isolated and used for TruSeq RNA library construction for transcriptome analysis. Samples were from 3 independent experiments. The library preparation and NGS data aquisition were performed by Macrogen (Macrogen, Inc., Korea)

2019-12-22 | GSE109077 | GEO

RNA sequencing of sorted immune cells from WT and CD4Cre-Yapfloxed mice from tumors and tumor-draining lymph nodes

Project description:We report the effect of T cell lineage-specific Yap deletion on tumor immunity in the B16F10 melanoma mouse model.

2019-12-11 | GSE139883 | GEO

RNA-sequencing of mouse melanoma cell lines WT31, B16F10 luc2, RET, D4M and HCmel12

Project description:In vitro cultured, sub-confluent (50 %) mouse melanoma cell lines WT31, B16F10 luc2, RET, D4M and HCmel12 were analyzed by RNA-seq.

2022-02-09 | GSE185539 | GEO

Impact of Staphylococcus aureus infection on the late lactation goat milk proteome: new perspectives for monitoring and understanding mastitis in dairy goats

Project description:This investigation reports a differential proteomic analysis of the goat milk to evaluate and understand the protein changes induced by Staphylococcus spp. during a subclinical intramammary infection (IMI). A number of 9 milk samples from multiparous goats were selected for the study, 3 of which in mid-lactation (30-60 Days in milk - DIM) with very low somatic cell count (SCC) from half-udders producing a sterile milk bacterial culture (MLU), 3 of which in late lactation samples (> 250 DIM) with SCC > 2,000,000 cells/mL from half-udders producing a sterile milk bacterial culture for the whole lactation (LHU) and in conclusion 3 in late lactation (> 250 DIM) with SCC > 2,000,000 cells/mL from goat half-udders with a milk bacterial culture repeatedly positive for Staphylococcus aureus (LHS). Samples were analyzed using a shotgun proteomics approach, based on filter-aided sample preparation (FASP) followed by LC-MS/MS and on differential analysis conducted by spectral count approach (1). (1) Pisanu S, Cacciotto C, Pagnozzi D, Puggioni GMG, Uzzau S, Ciaramella P, Guccione J, Penati M, Pollera C, Moroni P, Bronzo V, Addis MF. Proteomic changes in the milk of water buffaloes (Bubalus bubalis) with subclinical mastitis due to intramammary infection by Staphylococcus aureus and by non-aureus staphylococci. Sci Rep, 2019, 9 (1), 15850. Here, we reported both a characterization of goat milk proteins and a panel of differential proteins specific of S. Aureus-infected milk that mostly affected proteins involved in defense response processes and cytoskeleton organization. In conclusion, our results provide a depth characterization of milk proteins in goat samples uninfected and infected with S. Aureus, describe the changes induced by LHU and LHS subclinical intramammary infection and suggest indications to reveal subclinical staphylococcal mastitis in goat by a proteomic investigation of milk.

2020-04-09 | PXD017243 | Pride

Global gene expression profile of Japanese encephalitis virus(JEV) infected cytolytic B16F10 and Non-cytolytic JEV resistant B16F10r

Project description:B16F10, a murine melanoma cel line is cytolytic to JEV infection. We have identified a B16F10 cell line variant which is non-cytolytic to JEV infection. This variant cell line has two types of cells, one which is persistently infected JEV and another which is resistant to JEV infection. The JEV-resistant cells (B16F10r) were seperated from the presistently infected cells by single cell cloning. To understand the mechanism of JEV resistance microarray analysis was caried out to Identify and characterize genes differentially expressed during in uninfected/JEV-infected B16F10 and B16F10r cells. Agilent one-color experiment,Organism: Mus musculus ,Agilent Custom Mouse Whole Genome Mouse 8x60k Gene expression designed by Genotypic Technology Private Limited, Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

2013-08-01 | E-GEOD-42942 | biostudies-arrayexpress

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