Immune Variation Project (ImmVar)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA242428 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below.
2014-05-02 | GSE56035 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2014-05-02 | E-GEOD-56035 | biostudies-arrayexpress
Project description:Gene expression profiling of Monocytes (CD14+CD16-) from human peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from healthy individuals from the Boston area.
2014-05-02 | GSE56034 | GEO
Project description:Gene expression profiling of CD4 T-Cells (CD4+CD62L+) from human peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from healthy individuals from the Boston area.
2014-05-02 | GSE56033 | GEO
Project description:Gene expression profiling of Monocytes (CD14+CD16-) from human peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from healthy individuals from the Boston area. Over the course of 18 months, fresh blood samples from healthy participants were collected following a rigorous, standardized set of procedures (SOP). 15ml of blood was collected and used to isolate peripheral blood mononuclear cells (PBMCs). From the PBMCS, cell population of interest, CD14+CD16-, underwent a two-step sorting strategy in order to achieve cell purity >99%. mRNAs from these cells were profiled on Affymetrix GeneChip Human Gene ST 1.0 microarrays. Raw data CEL files were processed using the Robust Multichip Average (RMA) algorithm in Affymetrix PowerTools. To account for non-genetic factors such as batch effects, age, gender, and technical artifacts in gene expression data, we used Principal Component Analysis (PCA). PCs were estimated separately from the gene expression matrix for each population. The optimal numbers of PCs for association analysis were determined based on the PC that resulted in maximum number of cis-eQTLs. This procedure identified 20, 10, and 14 PCs in EU, EA and AA monocytes, respectively. GSE56034_GSM.ImmVarCD14.*.PC*.txt supplementary files: For each population EU, AA, and EA, individual PC-corrected matrices for samples that have passed both Expression QC and Genotyping QC. These are the same expression matrices that were used for the eQTL association analysis.
2014-05-02 | E-GEOD-56034 | biostudies-arrayexpress
Project description:Gene expression profiling of CD4 T-Cells (CD4+CD62L+) from human peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from healthy individuals from the Boston area. Over the course of 18 months, fresh blood samples from healthy participants were collected following a rigorous, standardized set of procedures (SOP). 15ml of blood was collected and used to isolate peripheral blood mononuclear cells (PBMCs). From the PBMCS, cell population of interest, CD4+CD62L+, underwent a two-step sorting strategy in order to achieve cell purity >99%. mRNAs from these cells were profiled on Affymetrix GeneChip Human Gene ST 1.0 microarrays. Raw data CEL files were processed using the Robust Multichip Average (RMA) algorithm in Affymetrix PowerTools. To account for non-genetic factors such as batch effects, age, gender, and technical artifacts in gene expression data, we used Principal Component Analysis (PCA). PCs were estimated separately from the gene expression matrix for each population and cell type. The optimal numbers of PCs for association analysis were determined based on the PC that resulted in maximum number of cis-eQTLs. This procedure identified 20, 12 and 12 PCs in EU, EA and AA CD4+ T-cells, respectively. GSE56033_GSM.ImmVarCD4.*.PC*.txt supplementary files: For each population EU, AA, and EA, individual PC-corrected matrices for samples that have passed both Expression QC and Genotyping QC. These are the same expression matrices that were used for the eQTL association analysis.
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Project description:Identification of genetic polymorphisms associated with inter-individual variation in immune response to Mycobacterium tuberculosis infection.
2011-12-30 | GSE34588 | GEO
Project description:Identification of genetic polymorphisms associated with inter-individual variation in immune response to Mycobacterium tuberculosis infection. We performed a genome-wide mapping study of loci that are associated with functional variation in immune response to MTB. Specifically, we characterized transcript and protein expression levels and mapped expression quantitative trait loci (eQTLs) in primary dendritic cells from 65 individuals, before and after infection with MTB
2011-12-06 | E-GEOD-34151 | biostudies-arrayexpress
Project description:Human twin studies have revealed the combined contribution of heritable and non-heritable (environmental) factors in shaping peripheral blood immune system variability. However, the heterogeneity within tissue immune compartments and the contribution of tissue-specific external factors remain unexplored. The human uterus is a tissue under constant regeneration exposed to distinct environmental factors. To assess uterine immune system variation, we have performed a transcriptomic and epigenetic analysis of uterine and peripheral blood immune cells in monozygotic twins and longitudinal samples in relation to heritable versus non-heritable factors.
2024-04-12 | GSE225040 | GEO
Project description:Identification of genetic polymorphisms associated with inter-individual variation in immune response to Mycobacterium tuberculosis infection. We performed a genome-wide mapping study of loci that are associated with functional variation in immune response to MTB (This dataset). We characterized transcript and protein expression levels and mapped expression quantitative trait loci (eQTLs) in primary dendritic cells from 65 individuals, before and after infection with MTB (see GSE34151).
2011-12-30 | E-GEOD-34588 | biostudies-arrayexpress