Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Quantifying epigenotype variations between mouse B and CD4+ T lymphocytes

ABSTRACT: This study aims at performing a genome wide comparative epigenomic and transcriptomic analysis of normal ex-vivo primary populations of lymphocytes of the adaptive immune system. Stocks of adult C57BL/6J mice are used for the isolation of pure and synchronous populations of resting B and nave CD4+ T-lymphocytes to avoid confounding cell cycle effects in our analysis. Integrative analysis of single-nucleotide 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) maps, histone marks and total stranded RNA-seq profiles have been performed to identify cell-type specific epigenetic signatures. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Mus musculus

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PROVIDER: E-ERAD-493 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:We develop a multivariate analysis of brain anatomy to identify the relevant shape deformation patterns and quantify the shape changes that explain corresponding variations in clinical neuropsychological measures. We use kernel Partial Least Squares (PLS) and formulate a regression model in the tangent space of the manifold of diffeomorphisms characterized by deformation momenta. The scalar deformation momenta completely encode the diffeomorphic changes in anatomical shape. In this model, the clinical measures are the response variables, while the anatomical variability is treated as the independent variable. To better understand the "shape-clinical response" relationship, we also control for demographic confounders, such as age, gender, and years of education in our regression model. We evaluate the proposed methodology on the Alzheimer's Disease Neuroimaging Initiative (ADNI) database using baseline structural MR imaging data and neuropsychological evaluation test scores. We demonstrate the ability of our model to quantify the anatomical deformations in units of clinical response. Our results also demonstrate that the proposed method is generic and generates reliable shape deformations both in terms of the extracted patterns and the amount of shape changes. We found that while the hippocampus and amygdala emerge as mainly responsible for changes in test scores for global measures of dementia and memory function, they are not a determinant factor for executive function. Another critical finding was the appearance of thalamus and putamen as most important regions that relate to executive function. These resulting anatomical regions were consistent with very high confidence irrespective of the size of the population used in the study. This data-driven global analysis of brain anatomy was able to reach similar conclusions as other studies in Alzheimer's disease based on predefined ROIs, together with the identification of other new patterns of deformation. The proposed methodology thus holds promise for discovering new patterns of shape changes in the human brain that could add to our understanding of disease progression in neurological disorders.

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Quantifying epigenotype variations between mouse B and CD4+ T lymphocytes

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