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  • Abf1 has been defined as a general regulatory factor involved in determining chromatin structure in the yeast Saccharomyces cerevisiae. As such, it plays a major role in a range of functions including DNA replication, transcriptional activation and gene silencing, as well as DNA repair. Previous studies have identified an Abf1 DNA consensus binding sequence and Abf1 binding at up to several hundred locations throughout the genome. Depletion of Abf1 in the cell, however, results in altered nucleosome structure at many thousands of sites throughout the yeast genome, suggesting a far greater role for Abf1 in chromatin structure and dynamics. Here, we examine genome-wide Abf1 binding using ChIP-Chip to measure its chromatin occupancy. Using a novel software package, Sandcastle, we detect 3,821 genomic positions at which Abf1 binds. We conducted a detailed bioinformatic analysis of these novel Abf1 binding sites, defining variations in the current consensus sequence and identifying many more genomic locations at which Abf1 can be found. These observations define the sites at which Abf1 occupancy determines chromatin structure, providing a framework for understanding how processes such as replication, transcription and DNA repair are organised within the genome.
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  • Desulfatibacillum alkenivorans AK-01 was grown on Hexadecane and Hexadecanoic acid. A microarray was run in triplicate for each growth condition and transcription was assessed for all predicted protein coding ORFs.
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  • Human cartilage taken from young normal knees following anterior cruciate ligament repair and osteoarthritic cartilage following total knee arthroplasty. Total RNA extracted using mirVana miRNA isolation kit (Life Technologies). The Affymetrix Flash Tag labelling kit was used to prepare samples for hybridisation onto Affymetrix miRNA 4.0 arrays.
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  • Daunorubicin (DNR) and Cytarabin (Ara-C) are the main chemotherapeutic drugs used for Acute Myeloid Leukemias (AML) treatment. However, their mode of action is not well understood. To decipher if these drug would induce rapid transcriptional reprogramming, we treated HL-60 AML cell line with DNR or Ara-C for 3 hours and carried out a transcriptomic analyses. In addition, we had shown that Reactive Oxigen Species (ROS) produced by NADPH oxidases (NOX) are involved in DNR-induced gene expression. We therefore also performed a transcriptomic analyses in HL-60 cells treated with DNR and VAS2870, an NADPH oxidase inhibitor. HL-60 cells were treated or not for 3 hours with 2 µM Ara-C, 1 µM DNR or 1 µM DNR + 20µM VAS 2870. RNAs were purified from 3 independent experiments and used to probe Affymetrix Human Gene 2.0 ST Genechips
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  • Expression profiling of Wilms tumour samples, which identified molecular signatures of the ureteric bud and collecting duct as well as those of the proximal and distal tubules in triphasic histology tumours. These observations indicate Wilms tumours can arise from a precursor cell capable of generating the entire kidney, such as the cells of the intermediate mesoderm from which both the metanephric mesenchym and ureteric bud are derived.
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  • Human cartilage taken from young normal knees following anterior cruciate ligament repair and osteoarthritic cartilage; old normal (protected) and old osteoarthritic (unprotected) following total knee arthroplasty. Total RNA extracted using mirVana miRNA isolation kit (Life Technologies). The Affymetrix Flash Tag labelling kit was used to prepare samples for hybridisation onto Affymetrix miRNA 4.0 arrays.
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  • Purpose: The goals of this study are to compare next-generation sequencing-derived hippocampal transcriptome profiling from mice lacking hippocampal Acetycholine release to evaluate the role of the neurotransmitter in hippocampal gene expression.
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  • Study aimed at evaluating differences in Du145, PC3 and LNCaP human prostate cancer cells treated with ATX-101 and docetaxel for 24h.
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  • Metastatic lesions of endometrial cancer. The data was firstly utilized for identification of highly connected and differentially expressed subnetworks between aggressive primary tumors and metastases. The 66 primary tumor samples have been reused from E-MTAB-2532 using the same prefix (4 digits) of Normalization Name.
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  • Statins, potent lipid-lowering drugs, were also shown to exert anti-proliferative activity. The aim of this study was to identify the biological pathways affected by changes in gene expression activity after statins treatment and to compare the results with observed anti-proliferative effects. The study was performed in vitro on a pancreatic cancer cell line MIA PaCa-2. The changes in gene expression were measured after 24 h of treatment by the statins (atorvastatin, lovastatin, simvastatin, fluvastatin, cerivastatin, pravastatin, rosuvastatin, and pitavastatin). The statins affected expression of a significant number of genes with mevalonate pathway, cell cycle regulation, and DNA replication being the most affected metabolic/signalling pathways.
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