Segmentation and intensity estimation for microarray images with saturated pixels
Ontology highlight
ABSTRACT:
ORGANISM(S): synthetic construct Homo sapiens
PROVIDER: GSE33899 | GEO | 2011/11/23
SECONDARY ACCESSION(S): PRJNA148259
REPOSITORIES: GEO
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Project description:Images and gpr files were examined using a novel saturation reduction method to determine whether accuracy could be improved by extending dynamic range of saturated pixels Three immunosignatures from human Valley Fever (Coccidiodes) patients and three immunosignatures from human influenza vaccine recipients were examined to test an algorithm that extends the apparent dynamic range of a fluorescence image. These images had several saturated spots at 70PMT and 100% laser power. The program examined the differences between Valley Fever and influenza in terms of standard image processing vs. segmentation and intensity estimation.
2011-11-23 | E-GEOD-33899 | biostudies-arrayexpress
Project description:Segmentation and intensity estimation for microarray images with saturated pixels
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Project description:Intake and absorption of cholesterol (the latter determined by double labeled cholesterol methodology) were nearly unchanged in mice fed the saturated fat diet, but the fecal excretion of neutral sterols (i.e. cholesterol and its microbial conversion products) was increased compared with control diet(+80%; p<0.01). The saturated fat diet did neither significantly affect biliary cholesterol secretion nor intestinal cholesterol absorption (49% vs. 65% in controls, double labeled water methodology, p>0.1). Thus, the increased fecal neutral sterol excretion was primarily due to increased net transintestinal cholesterol excretion (+89% versus control; p<0.05). Since a major fraction of TICE cholesterol absorption is normally reabsorbed (J Lipid Res 2019 Sep;60(9):1562-1572), the increased fecal cholesterol excretion could be due to more transintestinal excretion of cholesterol into the intestinal lumen and/or to its decreased reabsorption. The saturated fat diet increased jejunal expression of genes involved in cholesterol synthesis (Srebf2 and target genes), but did not affect whole body de novo cholesterol synthesis. Conclusion This proof-of-principle study shows that increasing the saturation of the dietary fat can stimulate fecal cholesterol excretion. Individual components of saturated fat diets are to be explored to address the responsible molecular mechanisms
2021-02-01 | GSE37097 | GEO
Project description:Astrocytes are essential regulators of the central nervous systems response to disease and injury and have been hypothesized to actively kill neurons in neurodegenerative disease. There has been intense interest in identifying the putative toxic factor(s) secreted by astrocytes. Here, we report a biochemical approach to isolate the astrocyte-derived toxic factor. Unexpectedly, instead of a protein, we found saturated lipids contained in ApoE/ApoJ lipoparticles as components of astrocyte-mediated toxicity in vitro and in vivo. Eliminating the formation of long-chain saturated lipids by astrocyte cell-type-specific knockout of the saturated lipid synthesis enzyme ELOVL1 mitigates astrocyte-mediated toxicity in vitro as well as in an acute axonal injury model in vivo. These results suggest a new mechanism by which astrocytes kill cells in the CNS.
2021-07-12 | MSV000087805 | MassIVE
Project description:Sample and RNA preparation: The series is composed of seventeen hybridizations for analysis of differentially expressed genes in placenta tissues from women after vaginal delivery (labouring) and after elective caesarean section (non-labouring). Total RNA extraction was performed by using the MagNa Pure Compact RNA Isolation Kit (Roche Applied Science). Labeling and hybridization: Total RNA was reverse transcribed and labeled with Cy3-attached dendrimer using the Genisphere 3DNA HS kit (Genisphere) as described in the manufacturer’s protocol. Hybridizations were carried out with a TECAN HS4800 instrument using the foramamide-based hybridization buffer from Genisphere containing 5% dextran sulphate and 0.5 microgram COT1 DNA/microgram RNA at 37°C for 23 hours. 3DNA dendrimer hybridizations were carried out in formamide-based hybridization buffer alone. Post-hybridization washes were carried out at room temperature with 2xSSC for 1 min, 0.2% SDS/2xSSC for 1 min and finally with0.2xSSC for 30 sec. Scanning, image analysis and data processing: The microarrays were scanned on an AXON 4000B scanner and images were quantified using GenePix pro 6.0 software. The background estimates were calculated using the morphological opening method. Spots that displayed a signal-to-noise ratio of less than 3 or that were significantly saturated (more than 20 % saturation among foreground pixels) were filtered out. The median was used as the averaging measure of the foreground pixels. After quality control, genes that were present in less than 50 % of the arrays were filtered out. Normalization was carried out using lowess normalization Sample labelling was balanced across the groups, presumably attenuating any dye-effect. For the purpose of finding differentially expressed genes empirical Bayes analysis, using the LIMMA package was applied. The data were analysed using a two-component linear model. The prior guess of the number of D.E genes was set to 0.01. Multiple testing was accounted for by estimating the false discovery rate. We applied the Benjamini-Hochberg procedure, as well as Storeys less conservative Q-value procedure was applied. In none of the cases were any genes significant at a reasonable (15-20% FDR) level. In summary, a 2.5-fold change in expression of any gene that was present on ≥ 8 arrays was considered significant, if the difference in fluorescence intensity between two groups reached a p-value of < 0.01. Keywords: Tissue samples of placenta from women after vaginal delivery (labouring) and after elective caesarean section (non-labouring)
2007-08-01 | GSE8375 | GEO
Project description:Gene expression pattern in murine 3T3-L1 adipocytes treated with saturated fatty acid (palmitate) in the presence or absence of PI3K p110alpha-selective inhibitor A66.
2020-01-01 | GSE129442 | GEO
Project description:The regulation of membrane lipid composition is critical for cellular homeostasis. Cells are particularly sensitive to phospholipid saturation, with increased saturation causing membrane rigidification and lipotoxicity. How mammalian cells sense membrane lipid composition and reverse fatty acid (FA)-induced membrane rigidification is poorly understood. Here we systematically identify proteins that differ between mammalian cells fed saturated versus unsaturated FAs. The most differentially expressed proteins were two ER-resident polytopic membrane proteins: the E3 ubiquitin ligase RNF145 and the lipid hydrolase ADIPOR2. In unsaturated lipid membranes, RNF145 is stable, promoting its lipid-sensitive interaction, ubiquitination and degradation of ADIPOR2. When membranes become enriched in saturated FAs, RNF145 is rapidly auto-ubiquitinated and degraded, stabilising ADIPOR2, whose hydrolase activity restores lipid homeostasis and prevents lipotoxicity. We therefore identify RNF145 as a FA-responsive ubiquitin ligase which, together with ADIPOR2, define an autoregulatory pathway that controls cellular membrane lipid homeostasis and prevents acute lipotoxic stress.
2022-08-10 | PXD034835 | Pride
Project description:The yeast Saccharomyces cerevisiae is a highly powerful model for systems genetics. While the advent of ordered deletion libraries has considerably facilitated yeast screening, it has also narrowed the diversity of screenable variants and precluded the exploration of the non-coding genome. Here, we present a versatile, time- and work-efficient method to functionally explore the yeast genome at an unprecedented throughput and resolution, using saturated transposon mutagenesis coupled to high-throughput sequencing. SAturated Transposon Analysis in Yeast (SATAY) allows the one-step mapping of all genetic loci in which a transposon can be inserted without disrupting a function necessary for cell growth. SATAY is especially suited to discover loci important for growth in various conditions. Here, we demonstrate that SATAY can be used to (2) reveal genetic interactions in single and multiple mutant strains, (1) reveal drug-resistant and -sensitive mutants, (3) detect not only essential genes, but also essential functional protein domains, and (4) generate not only null alleles, but also other informative genetic variants. Thus SATAY allows to easily explore the yeast genome at an unprecedented resolution and throughput.
2017-05-11 | E-MTAB-4885 | biostudies-arrayexpress
Project description:Impaired myocardial contractile function is a hallmark of heart failure (HF) which may present under resting conditions and/or during physiological stress. Previous studies reported that high fat feeding in HF is associated with improved myocardial contractile function at baseline. Our goal was to determine whether myocardial function is compromised in response to physiological stress and to evaluate the global gene expression profile of rats fed high dietary fat following infarction. Male Wistar rats underwent ligation or sham surgery and were fed normal (10% kcal fat) (SHAM+NC, HF+NC) or high fat (60% kcal saturated fat) (SHAM+SAT, HF+SAT) for 8 weeks. Myocardial contractile function was assessed using a Millar pressure-volume (PV) conductance catheter at baseline, during inferior vena caval occlusions and dobutamine (DOB) stress. Steady state indices of systolic function, left ventricular (LV)+dP/dtmax, stroke work and maximal power were increased in HF+SAT vs HF+NC; HF+NC were reduced vs SHAM+NC. Preload-recruitable measures of contractility [end systolic PV relationship, maximal elastance, preload recruitable SW and peak+dP/dtmax to end diastolic volume] were decreased in HF+NC but not HF+SAT. β-adrenergic responsiveness (delta-LV+dP/dtmax and delta-cardiac output DOB 0-10 µg•kg-1•min-1) was reduced in HF, but high fat feeding did not further impact contractile reserve in HF. Contractile reserve was reduced by high fat in SHAM+SAT. Microarray gene expression analysis reveals the majority of significantly altered pathways identified to contain multiple gene targets correspond to cell signaling pathways and energy metabolism. These findings suggest that high saturated fat improves myocardial function at rest and during physiological stress in infarcted hearts, but may negatively impact contractile reserve under non-pathological conditions. Furthermore, high fat feeding-induced alterations in gene expression related to energy metabolism and specific signaling pathways reveal promising targets through which high saturated fat potentially mediates cardioprotection in heart failure/LV dysfunction. Comparison of gene expression in heart failure or sham surgery hearts exposed to saturated or normal diets. Male Wistar rats (300-350g) were maintained on a reverse light-dark cycle and all procedures were done 3-6 hours into the dark phase cycle to synchronize with the normal active state of the rodents. Rats were randomly assigned to receive either a sham-operation (SH) or coronary ligation to induce cardiac dysfunction (HF). Heart failure was induced by ligating the left main coronary artery. Following surgery, rats were immediately fed either a normal rodent chow (NC) or a high saturated fat chow (SAT) with 60% caloric content derived from fat (25% palmitic, 33% stearic, 33% oleic acid, Research Diets).
2010-09-01 | E-GEOD-21021 | biostudies-arrayexpress