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Low-dimensional representation of variable DNA methylation sites across all placental and immune cell types and whole placental tissue samples shows samples cluster by cell type.

Journal: Epigenetics

Article Title: Placental and immune cell DNA methylation reference panel for bulk tissue cell composition estimation in epidemiological studies

doi: 10.1080/15592294.2024.2437275

Figure Lengend Snippet: Low-dimensional representation of variable DNA methylation sites across all placental and immune cell types and whole placental tissue samples shows samples cluster by cell type.

Article Snippet: To assess the performance of our placental DNA methylation deconvolution reference, we compared its ability to predict DNA methylation variation [ ] in a preprocessed placental whole tissue Illumina EPIC microarray DNA methylation dataset comprising 204 placentas across three cohorts (GEO accession number GSE232778) [ ] against the only existing multi-cell type reference [ ].

Techniques: DNA Methylation Assay

Analytic table of DNA methylation samples used for deconvolution reference.

Journal: Epigenetics

Article Title: Placental and immune cell DNA methylation reference panel for bulk tissue cell composition estimation in epidemiological studies

doi: 10.1080/15592294.2024.2437275

Figure Lengend Snippet: Analytic table of DNA methylation samples used for deconvolution reference.

Article Snippet: To assess the performance of our placental DNA methylation deconvolution reference, we compared its ability to predict DNA methylation variation [ ] in a preprocessed placental whole tissue Illumina EPIC microarray DNA methylation dataset comprising 204 placentas across three cohorts (GEO accession number GSE232778) [ ] against the only existing multi-cell type reference [ ].

Techniques: DNA Methylation Assay, Fluorescence

Placental cell type differential DNA methylation. Volcano plots comparing site-specific DNA methylation levels in one cell type against the average across all other cell types.

Journal: Epigenetics

Article Title: Placental and immune cell DNA methylation reference panel for bulk tissue cell composition estimation in epidemiological studies

doi: 10.1080/15592294.2024.2437275

Figure Lengend Snippet: Placental cell type differential DNA methylation. Volcano plots comparing site-specific DNA methylation levels in one cell type against the average across all other cell types.

Article Snippet: To assess the performance of our placental DNA methylation deconvolution reference, we compared its ability to predict DNA methylation variation [ ] in a preprocessed placental whole tissue Illumina EPIC microarray DNA methylation dataset comprising 204 placentas across three cohorts (GEO accession number GSE232778) [ ] against the only existing multi-cell type reference [ ].

Techniques: DNA Methylation Assay

Top differentially methylated sites unique to the five placental cell types (cytotrophoblast, endothelial, Hofbauer, stromal, and syncytiotrophoblast) and nucleated red blood cells with gene annotations reveal highly specific DNA methylation profiles by cell type.

Journal: Epigenetics

Article Title: Placental and immune cell DNA methylation reference panel for bulk tissue cell composition estimation in epidemiological studies

doi: 10.1080/15592294.2024.2437275

Figure Lengend Snippet: Top differentially methylated sites unique to the five placental cell types (cytotrophoblast, endothelial, Hofbauer, stromal, and syncytiotrophoblast) and nucleated red blood cells with gene annotations reveal highly specific DNA methylation profiles by cell type.

Article Snippet: To assess the performance of our placental DNA methylation deconvolution reference, we compared its ability to predict DNA methylation variation [ ] in a preprocessed placental whole tissue Illumina EPIC microarray DNA methylation dataset comprising 204 placentas across three cohorts (GEO accession number GSE232778) [ ] against the only existing multi-cell type reference [ ].

Techniques: Methylation, DNA Methylation Assay

Summary graphs of the root mean square error of prediction in the ability to model principal components of DNA methylation in 204 placenta dataset GSE232778 for our expanded reference versus the existing reference implemented in planet from 1,000 repeats of a 10-fold cross-validation linear regression model with estimated cell composition as the predictor variables.

Journal: Epigenetics

Article Title: Placental and immune cell DNA methylation reference panel for bulk tissue cell composition estimation in epidemiological studies

doi: 10.1080/15592294.2024.2437275

Figure Lengend Snippet: Summary graphs of the root mean square error of prediction in the ability to model principal components of DNA methylation in 204 placenta dataset GSE232778 for our expanded reference versus the existing reference implemented in planet from 1,000 repeats of a 10-fold cross-validation linear regression model with estimated cell composition as the predictor variables.

Article Snippet: To assess the performance of our placental DNA methylation deconvolution reference, we compared its ability to predict DNA methylation variation [ ] in a preprocessed placental whole tissue Illumina EPIC microarray DNA methylation dataset comprising 204 placentas across three cohorts (GEO accession number GSE232778) [ ] against the only existing multi-cell type reference [ ].

Techniques: DNA Methylation Assay, Biomarker Discovery