Gene expression signatures but not cell cycle checkpoint functions distinguish AT carriers from normal individuals and AT patients
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Tong Zhou
PROVIDER: E-GEOD-45850 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Transcriptional profiling of human lymphoblastoid cell lines with different ATM genotypes 6h post sham- or 1.5 Gy IR-treatmentl was compared to extract IR-related gene expression signatures that can identify ataxia telangiectasia (AT) carries from non AT carries and AT patients. Biological replicates: 6 or 4; Technical replicates: 2 with C3 and C5 dye swap.
2013-04-09 | E-GEOD-45849 | biostudies-arrayexpress
Project description:Transcriptional profiling of human lymphoblastoid cell lines with different ATM genotypes at basal level was compared to extract gene expression signatures that can identify ataxia telangiectasia (AT) carries from non AT carries and AT patients. Biological replicates: 4; Technical replicates: 2 with C3 and C5 dye swap.
2013-04-09 | E-GEOD-45848 | biostudies-arrayexpress
Project description:Acetaminophen can adversely affect the liver especially when overdosed. We used whole blood as a surrogate to identify genes as potential early indicators of an acetaminophen-induced response. In a clinical study, healthy human subjects were dosed daily with 4g of either acetaminophen or placebo pills for 7 days and evaluated over the course of 14 days. Alanine aminotransferase (ALT) levels for responders to acetaminophen increased between days 4 and 9 after dosing and 12 genes were detected with expression profiles significantly altered within 24hrs. The early responsive genes separated the subjects by class and dose period. In addition, the genes clustered patients who overdosed on acetaminophen apart from controls and also predicted the exposure classifications with 100% accuracy. The responsive genes serve as early indicators of an acetaminophen exposure and their gene expression profiles can potentially be evaluated as molecular indicators for further consideration. Randomized, single-blind, placebo-controlled, clinical study. Healthy male and female individuals from 18 â 58 years old weighing 55 kg to 85 kg volunteered as subjects in the study. Subjects were enrolled for 14 days each and were acclimated for 3 days on a controlled, standardized whole-food diet in order to assure a uniform nutritional intake. Starting on day 0 and until day 7 relative to the start of dosing, each subject received daily repeat dosing every 6 hrs (i.e. 4x daily) of either 1g of acetaminophen or placebo pills orally. Blood was collected at 8 a.m. on each day of the clinical study for alanine aminotransferase (ALT) measurement and complete blood counts (CBC).
2016-02-16 | E-GEOD-70784 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2016-02-16 | E-GEOD-70774 | biostudies-arrayexpress
Project description:Ires-GFP and CITED4-ires-GFP overexpressing permanent cell lines were generated by transfection of the CRC cell line SW480 with either the ires-GFP containing vector vector (in pCDNA4HISMAX) or the CITED4-ires GFP in (pCDNA4HISMAX) and selected with 2 ug/ ml puromycin in order to prepare permanent cell lines. For microarray analysis, the two cell lines were plated at a density of 1 x 10E5 cell in 12 well plates in 1 ml RPMI plus 10% FCS and penicillin/ streptomycin. The respective cell lines were harvested at day 1, 3 and 5 for RNA preparation and microarray analysis using Agilent human 4 x 44k expression microarrays. Every time point (cy3 labeled) was hybridzed together with Stratagene Human Total RNA standard as a control (cy5). Comparisons were made between the CITED4 overexpressing permanent cell line and ires-GFP containing cell line.
2014-11-01 | E-MTAB-2486 | biostudies-arrayexpress
Project description:The retention of a nucleus in the mature state of fish red blood cells (RBCs), and the ability to easily collect and manipulate blood in non-terminal experiments, makes it an ideal tissue on which to study the cellular stress response in fish. Through the use of the cGRASP 16K salmonid microarray, we are currently investigating differences in RBC global gene transcription in fish held under control conditions (12C) and exposed to heat stress (one hour at 25C followed by recovery at 12C). Repeated blood sampling (via a dorsal aorta cannula) enables us to examine the individual stress response over time. Samples were taken pre-heat stress (representing individual control) and at 4 and 24 hours post heat stress (representing early and late transcriptional regulation). A total of ~3000 features had significant signal when hybridized with RBC RNA derived targets and cannulation did not have a significant effect on RBC mRNA expression at the investigated time points. Genes involved in the stress response, immune response, and apoptosis were among those showing the highest dysregulation during both early and late transcriptional regulation. Additionally, genes related to the differentiation and development of blood cells were upregulated at the twenty-four hour time point. This study enables a broader understanding of the mechanisms underpinning the stress response in fish and the discovery of novel genes that are regulated in a stress specific manner. Moreover, salmonid transcripts that are consistently dysregulated in blood in response to heat stress are potential candidates of non-lethal biomarkers of exposure to this particular stressor. Two condition experiment, control (11C) and heat stressed fish (one hour at 25C followed by return to 11C). Six fish in each treatment. 3 repeated samples taken from each individual at time 0, 4 hours post heat stress and 24 hours. Common reference design used, with all experimental samples (control or heat stress) combined with reference pool RBC RNA on each array.
2010-09-21 | E-GEOD-21084 | biostudies-arrayexpress
Project description:TOX is a nuclear factor essential for the development of CD4+ T cells in the thymus. TOX is found to be aberrantly up-regulated in the skin biopsies and in the blood CD4+ T cells of cutaneous T cell lymphoma. The goal of this study is to identify potential transcriptional targets of TOX in CTCL by comparison between TOX shRNA transfected CTCL cells (Hut78 and HH) and control CTCL cells. Two color experiment. Lentivirus transduced control vector vs. TOX shRNA vectors on Hut78 and HH cell lines. Biological replicates: 3 control replicates, 3 shRNA tansduced replicates for each cell line.
2014-04-29 | E-GEOD-57122 | biostudies-arrayexpress
Project description:The availability of yeast DNA microarrays provides the possibility of monitoring gene expression levels as a function to toxin exposure, and consequently as a means of determining mechanisms of toxicity. This system possesses the benefit of the essential volume of yeast cultures, the high reproducibility of expression profiles, and the massive functional information. Because small amount of biological sample cultures are required for this analysis, toxicity test for rare chemical such as mycotoxins which is a natural compound and difficult to be artificially synthesized. Citrinin [518-75-2], 4,6-dihydro-8-hydroxy-3,4,5-trimethyl-6-oxo-3H-2-benzopyran-7-crboxylic acid, is the one of the popular mycotoxicin produced by Penicillium and Aspergillus family possibly spread all over the world. This natural chemicals is one of the well characterized mycotoxin but the information especially mechanism of toxic action is limited. We used two types of microarrays, one have ORF (Open reading Frame) fragment on the surface of the glass as probes and the other have probes as oligonucleotide probes on the microarray with 3 dimensions. We compared data properties and studied the toxicity of citrinin to yeast cells. Keywords: stress response Series containes 3 hybridization results from independent biological samples, and each experiment have high and low power scanned data respectively.
2010-06-10 | E-GEOD-6111 | biostudies-arrayexpress
Project description:Different Library Sample Preparation (LSP) allow the detection of a large common set of isoforms. However, each LSP also detects a smaller set of isoforms which are characterized both by lower coverage and lower FPKM than that observed for the common ones among LSPs. This characteristic is particularly critical in case of low input RNA NuGEN v2 LSP. The effect of statistical detection of alternative splicing considering low input LSP (NuGEN v2) with respect to high input LSP (TruSeq) was studied using a benchmark dataset, in which both synthetic reads and reads generated from high and low input LSPs were spiked-in. Statistical detection of alternative splicing was done using prototypes of bioinformatics analysis for isoform-reconstruction and exon-level analysis. Each available sample contains a total of 5 paired end replicates. 3 samples contain increasing numbers of spiked-in reads (20, 40, 80 millions) from NuGENv2 library preparation kit on a common TruSeq 1000ng background. 3 additional samples were built with the same approach, but spiked-in reads were collected from a TruSeq-based experiment. The remaining 6 samples follow the same approach of the previous 6, but the common background is based on a TruSeq library preparation on 100ng of material
2014-05-28 | E-GEOD-58001 | biostudies-arrayexpress
Project description:The data in this series forms the basis for the analysis presented in the above named paper. In this study, we used cDNA microarrays to ask if changes in gene expression are observed in response to a dietary shift in Drosophila melanogaster, a dietary generalist. Methods: Flies used in this study were derived from a multifemale collection at Iraklion, Crete, Greece, in August 2002 and reared in the laboratory for several generations. Three replicates were performed. At the start of each replicate, we collected 300 newly eclosed adults, separated them by sex, and stored them at low density in shell vials with standard cornmeal media for 3 days. Sexually mature males and females were placed together and allowed to mate. Mated females were allowed to oviposit overnight in chambers containing cornmeal medium filled Petri dishes (http://flyfood.arl.arizona.edu/cornmeal.php3). Hatching first instar larvae were reared for 36 hours on cornmeal medium in Petri dishes and then transferred to one of two conditions: 1) a control Petri dish consisting of cornmeal medium, or 2) an experimental Petri dish containing pure mashed banana. After 24 hours, larvae were plucked from these dishes, washed, transferred to microcentrifuge tubes in groups of 20, and flash frozen in liquid nitrogen. All samples were stored at -80C until RNA extraction. RNA was extracted from each tube using a Qiagen RNeasy kit (Qiagen, Inc., standard protocol). We used cDNA microarrays printed by the Genetic Analysis and Technology Core Custom Microarray Facility at the University of Arizona to assess expression levels. Printing material was amplified from BDGP Unigene library v1.0 containing 6K ESTs. Products were purified using Millipore Multiscreen filtration plates and re-suspended in 50%DMSO solution. Each product was printed in triplicate on Corning GAPSII aminosilane slides using a Virtek Chipwriter PRO microarray spotter. Between 10-15 micrograms of RNA were used for each reaction. RNA was reverse transcribed and labeled with one of two fluorescent dyes, Cy3 or Cy5 (details of protocol at http://gatc.arl.arizona.edu/Services/Microarray/aminoallyllabelling.html). Hybridization was completed on a Genomic Solutions Gentac automated hybridization station. Labeled material was allowed to hybridize to the array for 16 hours at 60°C. Wash conditions were: 1) low stringency wash twice at 50°C for 40seconds (1X SSC/ 0.2% SDS), 2) medium stringency wash twice at 42°C for 40 seconds ( 0.1X SSC/ 0.2% SDS), 3) high stringency wash twice at 42°C for 40 seconds (0.1X SSC). Hybridized arrays were scanned using the Applied Precision ArrayworxE slide scanner. We performed three independent hybridizations and three dye flips for a total of six arrays (2 treatments x 2 dyes x 3 replications = 12 samples, for 6 arrays). Each replicate consisted of an independent biological sample isolated on separate days. Identification of series: There are 18 series in this experiment. The second number in each series record represents the slide number (there were six slides used in this experiment). The third number in each series record represents the set on a given slide. For instance, for series record 331_2_1, these data correspond to slide 2, set 1. Each slide has 3 series numbers assoicated with it, representing set 1,2, or 3 on the slide. Each slide was paired with another in a "dye flip" experiment; thus, slides 2 and 3 were paired, slides 25 and 28 were paired, and slides 29 and 30 were paired. Keywords = dietary shifts Keywords = ecological genomics
2010-06-09 | E-GEOD-2687 | biostudies-arrayexpress