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Two condition experiment were compared: Wild type vs. E2f7/8 dko mouse liver. Biological replicates: two wild type replicates and two E2f7/8 dko replicates for each of 3-wk, 4-wk and 16-wk age groups.
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In this study, we used microarrays to investigate the gene expression program in conventional T cells, nTreg and conventional T cells treated with TGFbeta (iTreg) from wild-type mice and and mice having NFAT1/NFAT2 double-deficient (DKO) T cells. CD4+CD25- and CD4+CD25+ T cells were isolated by MACS and stimulated for 24 h with anti-CD3 and anti-CD28 antibodies in the absence or presence of TGFbeta. RNA was extracted and microarray analyses were performed. The data represents two independent biological replicates.
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Mapping of transposon mutant library during growth in Brain Heart Infusion (BHI) broth and BHI broth with 20 ug/ml ampicillin
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Comparison of human trabecular meshwork transcriptomes of cells overexpressing wild-type Myocilin
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Comparison of human trabecular meshwork transcriptomes of cells glaucoma-linked MYOC mutant Q368X
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Comparison of human trabecular meshwork transcriptomes of cells overexpressing glaucoma-linked MYOC mutant K423E
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A2780 ovarian cancer cells and a cisplatin resistant derivate of A2780 cells, obtained from ECACC, UK, No. 93112519 [A2780] and No. 93112517 [A2780 cis] were seeded out in T-75 flasks at a density of 2x106 for A2780sens and 3x106 for A2780cis cells in 15 ml of medium and preincubated overnight. Medium was removed and 15 ml fresh medium (37°C) with different concentrations of cisplatin, liposomal cisplatin or empty liposomes were added and incubated for 72 h at 37°C in a 5% CO2 incubator. In case of A2780sens cells, 1.72 µM cisplatin (IC50 concentration) and in case of A2780cis cells 8.94 µM cisplatin (IC50 concentration) were added. Liposomal formulations contained equal cisplatin concentrations. Empty liposomes were added in the same concentration as the liposomal cisplatin, to analyze the impact of liposomal lipids (A2780sens: 0.80µmol lipid, A2780cis: 4.15 µmol lipid). After incubation, medium was removed and cells were washed thrice with 10 ml PBS. 1 ml RLT-buffer was added and cells lysates were stored at -80°C until RNA extraction.
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Duplication of T is a known familial susceptibility determinant for chordoma. TO determine if a similar genetic alteration occurs in the sporadic disease a high-resolution array-CGH (Agilent custom-designed arrayCGH chip) was used to interrogate the chr 6q27 locus for duplication of T. Twenty two samples of chordoma and reference genomic DNA were hybridised to the chip including a positive control from a chordoma cell line.
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We compared genome-wide gene expression profiles of articular cartilage derived from 4 Kashin-beck disease patients and 4 Primary osteoarthritis. Total RNA was isolated from cartilage samples following by being amplified, labeled and hybridized to Agilent Human 4×44k Whole Genome microarray (G4112F).
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This study is about high content screening small molecule compound as radiosensitizer. Two compounds were got finally from a chemical bank. Our data indicate cancer cell lines became more sensitive to radiation after treatment with both two compounds respectively. In order to know the mechanism, microarray was performed to try to find the target genes of one compound. DU145 cells were treated with MS0019266 (5 umol/L) for 8 hours and total RNA was extracted from treated and untreated cells respectively. Synthesis of cDNA from total RNA and hybridization/scanning of microarrays were performed with Affymetrix GeneST1.0 array as described in the GeneChip manual. The raw intensity data were extracted from the GeneChip using Gene Expression Console ( Affymetrix Inc.) and normalized across the chips by log scale robust multi-array analysis (RMA) method and the quality control of each chip data was performed by investigating overall intensity values for all probes, negative and positive controls. To identify significantly differentially expressed genes between groups such as treated vs. control samples, Significance Analysis of Microarray (SAM, version2.1) was carried out. SAM is a widely-used microarray differential analysis tool that correlates gene expression data to a wide variety of clinical parameters and uses permutation to estimate False Discovery Rate for multiple testing. The cutoff of FDR q value for SAM test was set to 0.1. The gene expression data was also integrated with Gene Ontology functional database using DAVID to perform functional enrichment for better interpretation of gene expression profiles in the context of biological functions.
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