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Lineage-depleted (Lin-) cell and mono-nucleated cell (MNC), and uncultured and culture-derived colony forming unit-monocytes and megakaryocytes

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE40831 | GEO | 2012/09/13

SECONDARY ACCESSION(S): PRJNA175048

REPOSITORIES: GEO

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Lineage-depleted (Lin-) cell and mono-nucleated cell (MNC), and uncultured and culture-derived colony forming unit-monocytes and megakaryocytes

Project description:This SuperSeries is composed of the following subset Series: GSE40829: Expression profiles of lineage-depleted (Lin-) cell and mono-nucleated cell (MNC) samples derived from human umbilical cord blood GSE40830: Expression analysis of uncultured and culture-derived colony forming unit-monocytes and megakaryocytes Refer to individual Series

2012-09-13 | E-GEOD-40831 | biostudies-arrayexpress

Expression analysis of uncultured and culture-derived colony forming unit-monocytes and megakaryocytes

Project description:The cellular composition of heterogeneous samples can be predicted from reference gene expression profiles that represent the homogeneous, constituent populations of the heterogeneous samples. However, existing methods fail when the reference profiles are not representative of the constituent populations. We developed PERT, a new probabilistic expression deconvolution method, to address this limitation. PERT was used to deconvolve cellular composition of variably sourced and treated heterogeneous human blood samples. Our results indicate that even after correcting batch effects, cells presenting the same cell surface antigens display different transcriptional programs when they are uncultured versus culture-derived. Given gene expression profiles of culture-derived heterogeneous samples and profiles of uncultured reference populations, PERT was able to accurately recover proportions of pure populations composing the heterogeneous samples. We anticipate that PERT will be widely applicable to expression deconvolution problems using profiles from reference populations that vary from the corresponding constituent populations in cellular state but not cellular identity. Gene expression microarray to examine transcriptome variations between uncultured and culture-deried blood cells of the same phenotype as defined by the on and off expression of antigens.

2012-09-13 | GSE40830 | GEO

Expression analysis of uncultured and culture-derived colony forming unit-monocytes and megakaryocytes

2012-09-13 | E-GEOD-40830 | biostudies-arrayexpress

Lineage-depleted (Lin-) cell and mono-nucleated cell (MNC), and uncultured and culture-derived colony forming unit-monocytes and megakaryocytes

Project description:Lineage-depleted (Lin-) cell and mono-nucleated cell (MNC), and uncultured and culture-derived colony forming unit-monocytes and megakaryocytes

| PRJNA175048 | ENA

Expression profiles of lineage-depleted (Lin-) cell and mono-nucleated cell (MNC) samples derived from human umbilical cord blood

Project description:The cellular composition of heterogeneous samples can be predicted from reference gene expression profiles that represent the homogeneous, constituent populations of the heterogeneous samples. However, existing methods fail when the reference profiles are not representative of the constituent populations. We developed PERT, a new probabilistic expression deconvolution method, to address this limitation. PERT was used to deconvolve cellular composition of variably sourced and treated heterogeneous human blood samples. Our results indicate that even after correcting batch effects, cells presenting the same cell surface antigens display different transcriptional programs when they are uncultured versus culture-derived. Given gene expression profiles of culture-derived heterogeneous samples and profiles of uncultured reference populations, PERT was able to accurately recover proportions of pure populations composing the heterogeneous samples. We anticipate that PERT will be widely applicable to expression deconvolution problems using profiles from reference populations that vary from the corresponding constituent populations in cellular state but not cellular identity. Human umbilical cord blood-derived lineage negative cells and mononucleated cells

2012-09-13 | GSE40829 | GEO

Expression profiles of lineage-depleted (Lin-) cell and mono-nucleated cell (MNC) samples derived from human umbilical cord blood

Project description:The cellular composition of heterogeneous samples can be predicted from reference gene expression profiles that represent the homogeneous, constituent populations of the heterogeneous samples. However, existing methods fail when the reference profiles are not representative of the constituent populations. We developed PERT, a new probabilistic expression deconvolution method, to address this limitation. PERT was used to deconvolve cellular composition of variably sourced and treated heterogeneous human blood samples. Our results indicate that even after correcting batch effects, cells presenting the same cell surface antigens display different transcriptional programs when they are uncultured versus culture-derived. Given gene expression profiles of culture-derived heterogeneous samples and profiles of uncultured reference populations, PERT was able to accurately recover proportions of pure populations composing the heterogeneous samples. We anticipate that PERT will be widely applicable to expression deconvolution problems using profiles from reference populations that vary from the corresponding constituent populations in cellular state but not cellular identity. Human umbilical cord blood-derived lineage negative cells and mononucleated cells Cellular compositions of mononucleated cell and lineage negative cell compartments were deconvolved based on the gene expression profiles

2012-09-13 | E-GEOD-40829 | biostudies-arrayexpress

Brief report: Endothelial colony-forming cells and inflammatory monocytes in HIV.

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Gene expression profiles of endothelial cell colony forming unit cells derived from malignant breast disease patients and healthy controls

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Mono- and multi-nucleated ventricular cardiomyocytes constitute a transcriptionally homogenous cell population.

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Fibroblastic colony-forming unit bone marrow cells delay progression to gastric dysplasia in a helicobacter model of gastric tumorigenesis.

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