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PAN-INTACT enables generation of high-resolution chromatin accessibility maps.

By Samadrita Bhattacharyya (3878851), Adwait A. Sathe (6541643), Minoti Bhakta (3878854), Chao Xing (28961) and Nikhil V. Munshi (6541646)

Abstract

<p>A) Schematic diagram of experimental setup. CM nuclei were isolated from WT and Nkx2-5<sup>Cre/+</sup>; R26<sup>Sun1-2xsf-GFP-6xmyc/+</sup> P1 mouse hearts using 2.2M sucrose-cushion, an aliquot of which was used as the input sample. Remaining nuclei were subjected to MAN-IP using a Myc or PCM1 antibody. Chromatin accessibility maps were generated for each sample individually using the OMNI-ATAC-Seq protocol. B) Similarity matrix demonstrating high pairwise Pearson correlations for ATAC-Seq biological replicates and amongst different samples. C) Heatmap showing a high degree of overlap for accessible sites within input, PCM1, and Myc samples. As an additional comparison, DHS-seq data is shown for P1 mouse heart from the ENCODE dataset. Kb (Kilobases) D) Genome browser tracks for canonical markers of CMs (i, Myh6) and fibroblasts (ii, Col3a1) with ATAC-seq peaks for each sample and DHS-seq peaks for comparison. E) Gene Ontology (GO) analyses for annotated nearest neighboring genes surrounding ATAC-seq peaks from all 3 samples (i-iii) display terms related to cardiac growth and function. Displayed results represent GO terms only with False Discovery Rate (FDR) < 0.05.</p

Topics: Cell Biology, Genetics, Molecular Biology, Physiology, Biotechnology, Developmental Biology, Cancer, Hematology, Biological Sciences not elsewhere classified, ATAC, cell type-specific nuclei, cell type diversity, PAN-INTACT, cell type-specific functions, Transposase Accessible Chromatin, cell type isolation methods, R 26 Sun 1-2xsf mice, INTACT, cell types, high-fidelity chromatin accessibility maps, show cell type-specific isolation
Year: 2019
DOI identifier: 10.1371/journal.pone.0214677.g005
OAI identifier: oai:figshare.com:article/7939580
Provided by: FigShare
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