Lineage-depleted (Lin-) cell and mono-nucleated cell (MNC), and uncultured and culture-derived colony forming unit-monocytes and megakaryocytes
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE40831 | GEO | 2012/09/13
SECONDARY ACCESSION(S): PRJNA175048
REPOSITORIES: GEO
Similar Datasets
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
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
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. Fresh human umbilical cord blood-derived and serum free culture-derived colony-forming unit-monocytes (CFU-M) and megakaryocytes (MEGA) were compared respectively
2012-09-13 | E-GEOD-40830 | biostudies-arrayexpress
Project description:Lineage-depleted (Lin-) cell and mono-nucleated cell (MNC), and uncultured and culture-derived colony forming unit-monocytes and megakaryocytes
| PRJNA175048 | ENA
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
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| S-EPMC10288195 | biostudies-literature
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
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