Gene expressioin signatures in human lymphoblastoid cell lines with different ataxia telangiectasia-mutated (ATM) genotypes post sham- or IR-treatment
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Tong Zhou
PROVIDER: E-GEOD-45849 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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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.
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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.
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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
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Project description:Peripheral blood lymphocytes from a total of 15 healthy individuals without history of cancer (NoCa) were immortalized with Epstein-Barr virus. <br><br>Cells were exposed to mock treatment (Mock), ultra-violet radiation (UV), or ionizing radiation (IR). For UV radiation treatment, cells were exposed to 10 J/m^2 and harvested for RNA 24 hours later. For IR treatment, cells were exposed to 5 Gy of IR and harvested for RNA 4 hours later. For example, NoCa1-Mock refers to cells from healthy patient 1 exposed to mock treatment. The published manuscript (NAR 32:4786, 2004) can be found at http://nar.oupjournals.org/cgi/content/abstract/32/16/4786. <br><br>Data were analyzed with Affymetrix MAS version 4.0. <br><br>Normalization -- A reference data set was generated by averaging the expression of each gene over all data sets. The data for each hybridization were compared with the reference data set in a cube root scatter plot. A linear least-squares fit to the cube root scatter plot was then used to normalize each hybridization.
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