Measuring cell-type specific differential methylation in human brain tissue
Ontology highlight
ABSTRACT: We investigated genome-wide DNA methylation of NeuN+ and NeuN- fractions in three brain regions using comprehensive high throughput arrays for relative methylation (CHARM). We isolated genomic DNA from cell-sorted post-mortem brains using NeuN antibody and hybridized to Nimblegen microarrays (091020_HG19_CHARM_HX1 arrays).
Project description:Genome-wide DNA methylation was studied to determine whether iPS cells retain epigenetic memory at loci associated with its tissue of origin. We used custom Nimblegen microarrays to determine the genome-wide DNA methylation in mouse iPS cells. We isolated genomic DNA from mouse stem cells and hybridized to custom-designed Nimblegen microarrays (Me and CHARM arrays).
Project description:Genome-wide DNA methylation was studied to determine whether iPS cells retain epigenetic memory at loci associated with its tissue of origin. We used custom Nimblegen microarrays to determine the genome-wide DNA methylation in human iPS cells, ES cells, and somatic cells We isolated genomic DNA from human stem cells and somatic cells and hybridized to custom-designed Nimblegen microarrays (CHARM arrays).
Project description:Genome-wide DNA methylation of early and late passaged keratinocyte-derived iPS cells were compared to ES cells. We used custom Nimblegen microarrays to determine the genome-wide DNA methylation in human keratinocyte-derived iPS cells and ES cells We isolated genomic DNA from human stem cells and somatic cells and hybridized to custom-designed Nimblegen microarrays (CHARM arrays).
Project description:We investigated genome-wide DNA methylation during EMT in AML12 cells using comprehensive high throughput arrays for relative methylation (CHARM). We used custom Nimblegen microarrays. We isolated genomic DNA from cells at different timepoints post-TGF-β stimulation and hybridized to custom-designed Nimblegen microarrays (CHARM arrays). AML12 cells from 4 representative experiments were collected and used for the genome-wide DNA methylation analysis.
Project description:We investigated genome-wide DNA methylation of newly emerged queens, newly emerged workers, adult nurses, adult foragers and adult reverted nurses using comprehensive high throughput arrays for relative methylation (CHARM) We used custom Nimblegen microarrays We isolated genomic DNA from newly emerged queens, newly emerged workers, adult continuous nurses, adult continuous foragers and adult reverted nurses hybridized to custom-designed Nimblegen microarrays (CHARM arrays). Multiple brains were pooled for each sample and used for the genome-wide DNA methylation analysis.
Project description:This SuperSeries is composed of the following subset Series: GSE27134: DNA methylation data from human iPS cells, ES cells, cord blood, and keratinocytes GSE27186: Expression data of human somatic cell types and induced pluripotent stem cells GSE31742: DNA methylation data from human keratinocyte-derived iPS cells (N9) and ES cells Refer to individual Series
Project description:DNA methylation data from human tissues: 5 samples each of normal liver, frontal cortex, spleen and colon. 5 samples of colon tumor. Genomic DNA was isolated and hybridized to custom-designed Nimblegen microarrays (CHARM human array v1). 4 normal tissues and 1 colon tumor
Project description:This SuperSeries is composed of the following subset Series: GSE27968: DNA methylation data from AML12 cells during EMT GSE28291: Genome-scale epigenetic reprogramming during epithelial to mesenchymal transition Refer to individual Series
Project description:DNA methylation is often inversely correlated with gene expression. We used custom Nimblegen microarrays to determine the relationship between DNA methylation and gene expression in 6 iPS cell lines and the fibroblasts from which they were derived. We isolated genomic DNA from iPS cells and fibroblasts and hybridized to custom-designed Nimblegen microarrays (CHARM arrays).
Project description:We used custom Nimblegen microarrays to determine the DNA methylation profiles of iPS cells, ES cells, and fibroblasts. We isolated genomic DNA from iPS cells, ES cells, and fibroblasts and hybridized to custom-designed Nimblegen microarrays (CHARM arrays).