MicroRNA profiling by array of human skin melanoma and microenvironment
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Mariya Aksenenko
PROVIDER: E-MTAB-7060 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:B1 cells account for the majority of B cell population in the peritoneal cavity, and are essential for the innate immune responses and maintaining the homeostasis. The origin of the B1 cells and how to form the B1 cells pool in the postnatal life remain unknown. And the heterogeneity of B1 cells can largely affect the functions of B1 cells. Until now, nobody has performed the single cell RNA-seq of peritoneal B cells. In order to reveal the characteristics of peritoneal B cells, we have performed the scRNA-seq and scBCR-seq of the peritoneal B cells of mouse from different stages.
2022-05-21 | E-MTAB-10081 | biostudies-arrayexpress
Project description:We analyzed effects of monkeypox (MPX) and vaccinia (VAC) infection on cultured human cells. Our custom-designed arrays contain >18,000 human genes as well as genes for each open reading frame of MPX and VAC. A reference experiement design type is where all samples are compared to a common reference. Compound Based Treatment: Chemical used for treating infected cells Infection: Virus used for infection Cell Line: Cell line used for infection Time: Time cells were harvested after infection Keywords: reference_design Experiments used primary human monocytes with mock infection, VAC-Western Reserve, VAC-NYBOH, MPX-Zaire, gamma irradiated (killed) MPX-Zaire, and Ebola-Zaire (EBOV) (deposited March 2004). The next set of experiments used primary human monocytes (Mf7.29) and primary human fibroblasts (S100) with mock infection, VAC-Western Reserve, MPX-Zaire, and gamma irradiated MPX-Zaire (g-MPX) (deposited August 2004). The final set used primary human monocytes (Mph), primary human fibroblasts (NHDF), and HeLa cells with mock infection, VAC-Western Reserve, MPX-Zaire, and gamma irradiated MPX-Zaire (g-MPX). Some cells were treated with ionomycin + PMA (I+P), cycloheximide (CHX) or hydroxyurea (HU). (deposited November 2005). Total RNA from cells was harvested at each timepoint, preserved in Trizol, Trizol-extracted total RNA, 1 round amplified (Ambion MessageAmp I), directly labeled by Cy5 incorporation during reverse transcription of amplified RNA. Each sample was hybridized versus a common reference (Stratagene Universal Human Reference RNA plus a mix of poxvirus transcripts from all timepoints). The reference was1 round of amplification (Ambion MessageAmp I), directly labeled by Cy3 incorporation during reverse transcription of amplified reference RNA. Cy3 and Cy5 samples were hybridized to a custom human-poxvirus array. Fluorescent images of hybridized microarrays were acquired using the GenePix 4000B and GenePix 4200AL microarray scanners.
2008-07-17 | E-GEOD-11234 | biostudies-arrayexpress
Project description:With the goal of identifying changes in gene expression in CD4(+) T cells during the development of diabetes in the nonobese diabetic (NOD) mouse, we used DNA microarrays to analyze gene expression in CD4(+) T cells from the pancreatic draining lymph nodes of NOD/BDC 2.5 T cell receptor transgenic and WT NOD mice at different ages. At 4 and 6 weeks of age, we found up-regulation of a number of genes that are known to be induced by IFN-alpha. IFN-alpha levels and IFN-alpha-producing plasmacytoid dendritic cells were increased in the PLNs of 3- to 4-week-old NOD mice. Moreover, blockade of IFN-alpha receptor 1 in NOD mice by a neutralizing antibody at 2-3 weeks of age significantly delayed the onset and decreased the incidence of type 1 diabetes, increased the relative number of immature dendritic cells in the PLNs, and enhanced the ability of spleen CD4(+) T cells to produce IL-4 and IL-10. These findings demonstrate that IFN-alpha in the PLNs is an essential initiator in the pathogenesis of type 1 diabetes in NOD mice. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
2010-06-25 | E-GEOD-15213 | biostudies-arrayexpress
Project description:Three experiments, corresponding to the three figures in the article, are represented in this set. Each experiment was an ex vivo treatment time course as described in the paper. For each of the experiments, mRNA was isolated at the indicated time points, cDNA was directly prepared by reverse transcription in the presence of Cy5-labeled dUTP, and the expression profiled using Cy3-labeled cDNA prepared by reverse transcription of Stratagene Universal Human Reference RNA as a control. One experiment, corresponding to Figure 1 in the paper, is a set of infection, or mock-infection time courses, in which each of three cell types: primary human dermal fibroblasts, primary human macrophages, or HELA cells were respectively infected with Monkeypox virus, Vaccinia virus, or Ebola virus, or mock-infected. Infected cells or mock-infected cells were harvested and lysed at the indicated times after infection and mRNA isolated for analysis following the protocol described above. The second experiment, corresponding to Figure 2 in the paper, is a set of treatments of human dermal fibroblasts, each in 24-well plates with either: PBS only (mock), interferon alpha (IFN-alpha) at 0.6 pM final concentration (Sigma, St. Louis, MO), tumor necrosis factor alpha (TNF-alpha) at 0.6 pM final concentration (Sigma), PMA at 25ng/mL final concentration plus ionomycin at 1micromolar final concentration, polyinosinic-polycytidylic acid as potassium salt (poly(I-C)) at 100 microg/mL final concentration (Sigma), Escherichia coli 055:B5 lipopolysaccharide (LPS) at 1microg/mL final concentration (Sigma), or dexamethasone at 1 micromolar final concentration (Sigma). Cells were harvested and lysed at the indicated times and mRNA isolated for analysis following the protocol described above. The third experiment, corresponding to Figure 3 in the paper, is a set of infections or mock-infections of human dermal fibroblasts, or human primary macrophages, with Monkeypox virus or Vaccinia virus, respectively, followed by treatment with either ionomycin + phorbol myristic acid (PMA) or with poly(I-C). The intention of the experiment was to investigate whether prior infection altered the response of the cells to the chemical agents. Cells were harvested and lysed at the indicated times and mRNA isolated for analysis following the protocol described above. Description of sample characteristics: Time: Time after infection or Mock infection Infection: Ebola-Zaire/killed Monkeypox Virus/Mock infection/Monkaypox Virus/None/Pre infection/Vaccinia NY/Vaccinia WR Compound Based Treatment: Dexamethasone/Interferon-alpha/Ionomycin + PMA/LPS/PBS/polyinosinic-polycytidylic acid/TNF-alpha Cell Type: Primary Human Dermal Fibroblast/Primary Human Macrophage/HeLa Figure in article: Numbers group slides that are represented in the same figure of the article. A stimulus or stress experiment design type is where that tests response of an organism(s) to stress/stimulus. e.g. osmotic stress, behavioral treatment
2011-04-14 | E-GEOD-24125 | biostudies-arrayexpress
Project description:Mating is a complex process that causes many behavioral and physiological changes, but the factors triggering these changes and the underlying molecular processes are not well characterized. Honey bee queens provide a convenient system for dissecting these factors (e.g., physical manipulation, insemination volume, insemination substance) via instrumental insemination. We examined the effects of carbon dioxide (CO2), a commonly used anesthetic in instrumental insemination that causes changes similar to those observed after mating, and physical manipulation, which presumably mimics the act of copulation, on the brain transcriptional changes in honey bee queens. We found significant gene overlap between our study and previous mating studies in honey bee queens and Drosophila. This suggests that molecular pathways regulating the mating process are conserved across different mating regimes of honey bees as well as across insect orders.
2011-01-30 | E-MEXP-2646 | biostudies-arrayexpress
Project description:Hypoxia results in the changes in expression of many genes, the majority of which are mediated via the transcriptional activity of the hypoxia inducible factor (HIF) complex. However, other mechanisms of gene regulation by hypoxia are likely and include control of mRNA stability, regulation of mRNA translation and regulation mediated by micrornas. The aim of this study is to identify microRNAs which expression is regulated by hypoxia. We chose the breast cancer line MCF7 for study as we had previously characterised the expression of the components of the HIF system in that cell line and undertaken an extensive study of the gene expression profile in response to hypoxia, a prolyl hydroxylase inhibitor dimethyloxalylglycine and HIF-1a isoform manipulations (Eldvidge. G.P. et al. (2006) JBC, vol. 281, 22, 15215-15226).
2008-03-01 | E-MEXP-1111 | biostudies-arrayexpress
Project description:The aim of this study was to identify alarm (fast) and acclimation phase (delayed) changes in the gene expression pattern in leaves of maize (CM 109 genotype) subjected to moderate chilling for 28 hours.
2009-11-01 | E-MEXP-1865 | biostudies-arrayexpress
Project description:Identification of the régulation pathways implied in adventitious root formation control in Arabidopsis etiolated seedlings. 2 mutants : a null allele and a weak allele of the ARGONAUTE gene. 4 repetitions in 2 pools for each sample.
2006-08-23 | E-MEXP-790 | biostudies-arrayexpress
Project description:Transcriptome analyses of the fission yeast Schizosaccharomyces pombe cells lacking the CSL transcription factor cbf11. Wild-type cells were used as a control. Both genotypes were analyzed when grown to exponential phase in the complex YES medium, or in YES supplemented with ammonium chloride. The aim was to identify Cbf11-regulated genes, and cbf11-associated phenotypes are affected by the presence of a good nitrogen source.
2024-04-05 | E-MTAB-13302 | biostudies-arrayexpress
Project description:97 triple negative tumors were selected from the fresh-frozen tissue bank of the Netherlands Cancer Institute and gene expression profiles were generated using 35K oligonucleotide microarrays. Human breast carcinomas were snap frozen in liquid nitrogen within one hour after surgery and stored in the fresh-frozen tissue bank of the Netherlands Cancer Institute. RNA from a pool of more than 100 unselected fresh frozen breast carcinomas were isolated and pooled to form the reference to which each individual breast carcinoma is hybridized.
2007-10-09 | E-NCMF-2 | biostudies-arrayexpress