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  • We aimed to identified genes whose expression was changed after 48 hours of 3 µM 5-aza treatment in HPV+ head and neck cancer cell lines UMSCC47 and SCC090, or in osteosarcoma cells line U2OS using Illumina microarray gene expression profiling. 1 million of UMSCC47, SCC090 or U2OS cells were treated or not with 3 µM of 5-aza in independent triplicate for 48h; RNA was extracted and analyzed on Human HT gene expression array at Yale Genomics facility.
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  • mESC adapted to 2i/LIF conditions over four passages (8 days) before differentiation towards the neuronal lineage was induced using experimental conditions described in the literature (PMID: 12524553).
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  • Beta-cell proliferation is enhanced in the mice treated with with adenovirus containing constitutively active mutant of MEK1 (CAM mice) than mice treated control adenovirus. This microarray anaslysis was performed for the purpose of exploring the molecular mechanism thereby beta-cell proliferation is enhanced in L-MEK mice.
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  • Zebrafish ncx1h (also known as slc8a1a) encodes a cardiac specific sodium-calcium exchanger 1 (NCX1h), a primary Ca 2+ efflux effector in cardiomyocytes. The zebrafish tremblor (tre) mutant lacks functional NCX1h and, consequentially, cyclic Ca2+ transients are abolished. In this study, we investigated the effect of aberrant Ca2+ homeostasis in cardiomyocytes on gene expression. Wild type and ncx1 mutant hearts at 48 hours post fertilization were isolated for RNA preparation and gene expression analysis was performed using an Affymetrix Zebrafish GeneChip.
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  • Bhlhe23 is a transcription factor that is required for the maturation and survival of retinal rod bipolar cells in mice. In the adult Bhlhe23-/- retina, rod bipolar cells are almost completely absent. We identified genes that were likely to be important to rod bipolar cell maintenance and function by identifying genes that were significantly down-regulated in the transcriptome of adult Bhlhe23-/- mouse retina compared with wild type retina.
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  • Wild type mouse hippocampi from a total of 186 animals of both genders and two background strains (C57Bl/6 and 129s5) between the ages of 58 to 600 days
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  • Spleens from the B6 mice were isolated and single cell suspension was made. CD4 T cells were purified from the splenocytes using magnetic bead separation. Briefly, Splenocytes were incubated with biotinylated antibody cocktail consisting of antibodies (Biolegend) to CD19, B220, CD11b, CD11c, NK1.1, Gr1, CD25 CD8. After a wash step, cells were incubated with streptavidin conjugated magnetic particles (BD Biosciences). After washing, CD4 T cells were isolated by applying a magnetic field and removing the untouched cells. Purified CD4 T cells were then activated with plate-bound anti-CD3 plus anti-CD28 in presence of either Th1 or Th17 or Th1/17 polarizing condition for 3 days. Total RNA from the 3 days differentiated Th1, Th17 and Th1/17 cells was isolated using mirVana miRNA isolation Kit (Invitrogen).
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  • C2C12 myoblasts were seeded at a density of 25,000 cells/cm2 in a 10cm cell culture dish and differentiated with low serum differentiation medium at 37 °C, 5% CO2 for 72h and further treated with either DB or recombinant Irisin protein (1000ng/ml) for 6h, 12h, 24h and 48h. Myotubes were resuspended in 2ml of TRIzol ® for each 10cm dish and RNA isolation was performed according to the manufacturer s protocol. Purified isolated RNA was then subjected to Illumina bead array sequencing and data analysis, as per in-house protocols (Sciencewerke, Singapore). Only genes that were upregulated or downregulated by 1.5-fold were considered significant. For genes that had multiple probes (with different accession number), only one probe with the highest upregulation or downregulation was taken into consideration.
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  • Transcriptional profiling of peripheral blood mononuclear cells (PBMCs) from 30 subjects collected at day 0, day 1 and day 3 post yellow fever (YF) vaccination. Each patient sample is performed in duplicate to reduce the chance of error. Briefly, the project investigates how cross-reactive JE antibodies that are generated from prior vaccination can influence YF live-attenuated vaccine (LAV). The groups are hence segregated based on the YF antibody titers after 1 month vaccination. Group 4 refers to the control group where individuals received only the YF LAV. Enhancing group refers to the treatment group (given JE followed by YF vaccine), where individuals had YF antibody titers higher than 99% confidence interval of the YF antibody titers of the control group. Non-enhancing group, on the other hand, refers to the treatment group where individuals had YF antibody titers within or lower 99% confidence interval of the control group. Our present study provides evidence that enhancing levels of cross-reactive antibodies from prior Japanese encephalitis (JE) vaccination can improve subsequent YF immunogenicity. These microarray results indicate the genes and gene signatures that are associated with the differences in YF immunogenicity.
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  • Here we established two tumor tissue-derived long-term-cultured breast cancer stem cells (BCSC). RNA extraction and microarray analysis total RNA from BCSC treating with G1, G15, or control (Ctrl) for 48 hr were extracted using Trizol Reagent. Important significant differences of cDNA genes were identified. (The G1-treated group was designed as \"12\", the control group was \"11\" (raw data: 11 and 12; processed data: BCSC-G1). Similarly, the G15-treated study group was defined as \"14\", the control group was \"13\" (raw data: 13 and 14; processed data: BCSC-G15).
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