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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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The effect of cell subset isolation method on gene expression in leukocytes.

ABSTRACT: Analysis of the effect of isolation methods (fluorescence activated cell sorting (FACS), positive and negative immunomagnetic selection) on gene expression in human primary CD4+, CD8+ T cells, B cells and monocytes. FACS incurs the least short-term changes in gene expression signature. This study evaluated the short-term effects on gene expression in four leukocyte subsets (CD4+, CD8+ T cells, B cells and monocytes) of the three commonly used isolation methods (FACS, positive and negative selection) in order to identify the optimal method for cell isolation for gene expression studies in patient samples where gene expression pertaining to a disease state or treatment is of interest and gene expression caused by cell handing is minimized.

ORGANISM(S): Homo sapiens

SUBMITTER: Nadejda Beliakova-Bethell

PROVIDER: E-GEOD-50008 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The effect of cell subset isolation method on gene expression in leukocytes.

Project description:Analysis of the effect of isolation methods (fluorescence activated cell sorting (FACS), positive and negative immunomagnetic selection) on gene expression in human primary CD4+, CD8+ T cells, B cells and monocytes. FACS incurs the least short-term changes in gene expression signature.

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Transcriptome comparison between thymic T cell subsets in wildtype and Caph2(I15N) mutant mice

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Aire regulates transfer of antigen from mTEC to dendritic cells for induction of thymic tolerance

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Project description:The aim of this study was to identify differential gene expression in lung T cell subsets upon germline Serpinb1a ablation. CD8-CD19- lymphocytes enriched by negative selection from digested lungs of naÃ¯ve, 9-12 week old wild-type 129S6 mice or Serpinb1a homozygous null mice were FACS sorted into CD4+ CCR6+ effector/ memory T cells, gd T cells, or CD4+ CD25hiCD127low regulatory T cells. FACS sorted cells were collected into RLT buffer (Qiagen) directly, lysed, and total mRNA was isolated using Quiagen's RNeasy mini kit. Wild-type vs. Serpinb1a-/- gd+ T cells, CD4+ CCR6+ effector/ memory T cells, or CD4+ CD25hiCD127low regulatory T cells

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Suberoylanilide hydroxamic acid (SAHA) induces limited changes in the transcriptome of primary CD4+ T cells

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Project description:Negative immunomagnetic selection has become the method of choice for isolating T cell subsets for functional studies due to concerns that directly binding antibody to the surface of a cell, as occurs with positive selection, results in cross-linking of surface antigens, altered gene transcription and subsequent cellular activation. However there is little data to support this. We therefore examined the impact of the method of immunomagnetic cell selection on the gene expression profile of healthy human CD4 and CD8 T cells in a total of 21 cases. Experiment Overall Design: This study was composed of 4 groups of samples: CD4 Negative Selection (n=5), CD4 Positive Selection (n=5), CD8 Negative Selection (n=5), CD8 Positive Selection (n=6). Two samples (PS6 CD8 and PS9 CD4) were removed from the analysis due to discrepant normalised unscaled standard errors

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Blood Transcriptional Profiles of Active TB (UK Test Set Separated)

Project description:This dataset aims to dissect the whole blood transcriptional signature by determining if elements of the whole blood signature are still present in purified cell subpopulations. We aimed to characterise the transcriptional response during TB and identify if cell subsets drove changes in whole blood cellular composition. The aim of the experiment was to define transcriptional signatures in neutrophils, monocytes, CD4+ and CD8+ cells from blood of active TB patients and healthy controls to distinguish the signature of active TB patients from each other and from healthy controls. This will help in the diagnosis of active tuberculosis, which normally relies on culture of the bacilli, which can take up to 6 weeks, sometimes the bacilli cannot be obtained from sputum thus requiring invasive techniques obtaining bronchoalveolar lavage (BAL). In some cases the bacill cannot be grown from sputum or BAL. Experimental design : Whole blood collected in EDTA tubes from patients with active TB disease and healthy controls. Blood was then processed or separated sequentially into neutrophil, monocyte, CD4+ or CD8+ populations and then processed. All patients were sampled prior to the initiation of any antimycobacterial therapy. Active pulmonary TB: PTB - all patients confirmed by isolation of Mycobacterium tuberculosis on culture of sputum or bronchoalvelolar lavage fluid. Healthy controls - these were volunteers without exposure to TB who were negative by both tuberculin skin test (<15mm if BCG vaccinated, <6mm if unvaccinated); who were also negative by IGRA (as described above). This dataset: PTB, n = 7 patients (whole blood, neutrophils, monocytes, CD4+ or CD8+). BCG+, n = 4 patients (whole blood, neutrophils, monocytes, CD4+ or CD8+). Experimental variables : Patient group: Active PTB; Healthy controls (BCG vaccinated only) and Cell populations: Neutrophils, Monocytes, CD4+, CD8+. Ethnicity - a range of ethnic groups is represented.

2010-08-11 | E-GEOD-19443 | biostudies-arrayexpress

Gene expression analysis of thymocyte subsets

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microRNA expression profiling of various C57Bl/6 myeloid cell populations

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