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Purified human leukocyte subtype DNA methylation profiles

ABSTRACT: The objective of the study was to identify differentially methylated regions of DNA (DMRs) that distinguish human leukocyte subtypes, and hence serve as biomarkers for those immune cell types. This file contains Illumina Infinium HumanMethylation27 BeadChip data for human leukocyte subtypes that were purified from whole blood samples via magnetic activated cell sorting (MACS) and purity confirmed by flourescence activated cell sorting (FACS).

ORGANISM(S): Homo sapiens

PROVIDER: GSE39981 | GEO | 2012/11/05

SECONDARY ACCESSION(S): PRJNA172201

REPOSITORIES: GEO

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Purified human leukocyte subtype DNA methylation profiles

Project description:The objective of the study was to identify differentially methylated regions of DNA (DMRs) that distinguish human leukocyte subtypes, and hence serve as biomarkers for those immune cell types. This file contains Illumina Infinium HumanMethylation27 BeadChip data for human leukocyte subtypes that were purified from whole blood samples via magnetic activated cell sorting (MACS) and purity confirmed by flourescence activated cell sorting (FACS). Bisulphite converted DNA from the 73 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

2012-11-05 | E-GEOD-39981 | biostudies-arrayexpress

VeraCode GoldenGate Methylation Assay microarray data for purified human leukocytes, reconstruction mixtures and human whole blood samples

Project description:The objective of the study was to utilize DNA methylation to quantify human leukocyte subsets in human blood. This file contains data from an Illumina custom VeraCode GGMA microarray for human leukocyte subtypes (purified from whole blood samples via magnetic activated cell sorting (MACS) and purity confirmed by flourescence activated cell sorting (FACS)) as well as for complex mixtures of DNA from those samples, and for human whole blood samples.

2014-02-04 | GSE54647 | GEO

VeraCode GoldenGate Methylation Assay microarray data for purified human leukocytes, reconstruction mixtures and human whole blood samples

2014-02-04 | E-GEOD-54647 | biostudies-arrayexpress

Comparison of microglial proteomes of MACS and FACS-based purified CD11b+ microglia

Project description:Background Proteomic characterization of microglia has been limited by low yield and contamination by non-microglial proteins by magnetic-activated cell sorting (MACS) enrichment strategies. To determine whether a fluorescent-activated cell sorting (FACS)-based strategy overcomes these limitations, we compared microglial proteomes of MACS and FACS-based purified CD11b+ microglia in order to identify core sets of microglial proteins in adult mouse brain tissue. Results Quantitative multiplex proteomics by tandem mass tag mass spectrometry (TMT-MS) of MACS-enriched (N = 5) and FACS-purified (N = 5) adult wild-type CD11b+ microglia identified 1,791 proteins, of which 953 were differentially expressed indicating significant differences between both approaches. While the FACS-purified microglia proteome was enriched with cytosolic, endoplasmic reticulum and ribosomal proteins involved in protein metabolism and immune system functions, the MACS-enriched microglia proteome was enriched with proteins related to mitochondrial function and synaptic transmission. As compared to MACS, the FACS microglial proteome showed strong enrichment for canonical microglial proteins while neuron, astrocyte, and oligodendrocyte proteins were decreased. Interestingly, we observed enrichment of endothelial specific proteins in the FACS microglia proteome. By comparing FACS-purified microglia proteomes with transcriptomes, we observed highly concordant as well as highly discordant proteins that were abundant at the protein level but low at the transcript level. Conclusions We demonstrate that TMT-MS proteomics of FACS-purified adult microglia is superior to column-based enrichment approaches, resulting in purer and highly-enriched microglial proteomes. We also define core sets of highly-abundant adult microglial proteins including Moesin (Msn) that can guide future studies.

2020-05-11 | PXD015652 | Pride

FACS purified cortical projection neurons

Project description:3 subtypes of cortical projection neurons were purified by fluorescence-activated cell sorting at 4 different stages of development from mouse cortex. A detailed description of the data set is described in Arlotta, P et al (2005). Keywords = corticospinal motor neuron callosal corticotectal cortex development FACS

2005-01-19 | GSE2039 | GEO

Transcription profiling of mouse FACS purified cortical projection neurons

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miRNA profiling of FACS sorted human leukocyte cell types

Project description:Affymetrix miRNA arrays were used to generate miRNA profiles of peripheral blood leukocytes and FACS sorted neutrophils, monocytes, B-cells, T-cells, CD4+ T-cells, and CD8+ T-cells, being the major leukocyte cell types in human. The study allowed for the determination of the miRNAs that were expressed in each leukocyte cell subtype. Two-way hierarchical clustering on the miRNAs and samples illustrated that miRNA expression profiles of B- and T-cells were very much alike, and that there there were a number of miRNAs which appeared to have an expression profile specific to certain leukocyte cell subtypes. This study will facilitate the identification of microRNAs associated with and contributing to single leukocyte cell subtypes.

2009-11-26 | GSE19183 | GEO

miRNA profiling of FACS sorted human leukocyte cell types

2010-05-19 | E-GEOD-19183 | biostudies-arrayexpress

Characterization of MACS isolated microglia cells (CD11b positive cells) in comparison to all non-CD11b positive cells (termed non-target cell fraction (NTCF)) with proteomics

Project description:Microglia isolation from adult mouse brains remains difficult in comparison to microglia isolation from brains from newborn mouse brains as connective tissue, extracellular matrix materials and thicker myelin sheaths substantially influence traditional isolation protocols used with newborn mouse brains. Since the introduction of magnetic activated cell sorting (MACS), it has been reported that it is possible to also obtain microglia cells from adult mouse brains with a very good purity. However, most studies only used flow cytometry and/or qPCR to determine microglia enrichment and enrichment of traditional microglia marker proteins. Therefore we wanted to characterize in an unbiased way the proteomes of with MACS isolated microglia cells (CD11b positive cells) in comparison to all non-CD11b positive cells (termed non-target cell fraction (NTCF)), which consist of primarily astrocytes, neurons and oligodendrocytes. Therefore, we isolated from three adult mouse brains via MACS CD11b positive cells as well as the remaining CD11b negative cells (NTCF) to characterize the proteome of both cell fractions. The obtained proteomes were compared to a dataset of proteomic signatures for all CNS cell types determined by Sharma et al., (2015, doi: 10.1038/nn.4160) to determine the amount of enrichment of microglia-specific proteins.

2024-03-22 | PXD031973 | Pride

Transcriptomic characterization of the human cell cycle in individual unsynchronized cells

Project description:Here, we profiled transcription across the cell cycle in single human myxoid liposarcoma cells, without prior synchronization. Flourescence-activated cell sorting was used to infer G1, S or G2/M cell cycle stages after staining cells for DNA content. Single-cell RNA-sequencing was performed according to the Smart-seq2 protocol.

2017-11-09 | E-MTAB-6142 | biostudies-arrayexpress

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