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Fig. 2 | BMC Medicine

Fig. 2

From: Choice of surrogate tissue influences neonatal EWAS findings

Fig. 2

Infant cord tissue is a better surrogate for primary tissues of mesenchymal stem cell (MSC)-derived mesodermic germinal origins, while infant cord blood is a better surrogate for primary tissues of hematopoietic stem cell (HSC)-derived mesodermic germinal origins: hierarchical clustering of GUSTO tissues (cord tissue, cord blood) with 25 primary tissues/cells profiled using reduced representation bisulfite sequencing in the Epigenome Roadmap project. Infant cord tissue clustered more closely with primary tissues of MSC-derived mesodermic germinal origins, while infant cord blood clustered more closely with primary tissues of HSC-derived mesodermic germinal origins. Left panel shows heatmap of DNA methylation values, with each row representing each tissue type and each column representing each CpG. Color changes from yellow to blue as DNA methylation changes from 0% to 100%. Right panel of plot shows dendrogram, with tissue types of ectodermic, endodermic, HSC-derived mesodermic, and MSC-derived mesodermic germinal origins represented in light pink, light purple, light turquoise, and light orange, respectively; GUSTO cord tissue and cord blood are represented in bright orange and bright blue, respectively. DNA methylation values from GUSTO tissues were generated using Infinium 450 K array (for each CpG and tissue type, the median value across all samples was used). For tissues/cells profiled by the Epigenome Roadmap project, only DNA methylation sites with a minimum reads coverage of 30X were retained and reads from both strands were combined. Hierarchical clustering was performed using only CpG sites that passed quality control filtering in GUSTO tissues, were non-missing in at least 10 out of the 25 Epigenome Roadmap samples, and had interquartile range greater than 10% across different Epigenome Roadmap tissues/cells

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