Single Cell Spatial Chromatin Analysis of Fixed Immunocytochemically Identified Neuronal Cells Article Swipe

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Jaehee Lee , Youtao Lu , Jinchun Wang , Jifen Li , Stephen Fisher , C. Erik Nordgren , Jean G. Rosario , Stewart A. Anderson , Alexandra V. Ulyanova , Steven Brem , H. Isaac Chen , John A. Wolf , M. Sean Grady , Mimi Healy , Junhyong Kim , James Eberwine ·

YOU? · · 2019 · Open Access · · DOI: https://doi.org/10.1101/780387

Assays examining the open-chromatin landscape in single cells require isolation of the nucleus, resulting in the loss of spatial/microenvironment information. Here we describe CHEX-seq ( CH romatin EX posed) for identifying single-stranded open-chromatin DNA regions in paraformaldehyde-fixed single cells. CHEX-seq uses light-activated DNA probes that binds to single-stranded DNA in open chromatin. In situ laser activation of the annealed probes’ 3’-Lightning Terminator™ in selected cells permits the probe to act as a primer for in situ enzymatic copying of single-stranded DNA that is then sequenced. CHEX-seq is benchmarked with human K562 cells and its utility is demonstrated in dispersed primary mouse and human brain cells, and immunostained cells in mouse brain sections. Further, CHEX-seq queries the openness of mitochondrial DNA in single cells. Evaluation of an individual cell’s chromatin landscape in its tissue context enables “spatial chromatin analysis”. One Sentence Summary A new method, CHEX-seq ( CH romatin eX posed), identifies the open-chromatin landscape in single fixed cells thereby allowing spatial chromatin analysis of selected cells in complex cellular environments.

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Computational Biology

Cell (Biology)

Molecular Biology

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Chromatin Biology Cell biology DNA Single-cell analysis ChIA-PET Computational biology Cell Molecular biology Genetics Nucleosome

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Type: preprint
Language: en
Landing Page: https://doi.org/10.1101/780387
PDF: https://www.biorxiv.org/content/biorxiv/early/2019/09/24/780387.full.pdf
OA Status: green
References: 50
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DOI: https://doi.org/10.1101/780387

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Title: Single Cell Spatial Chromatin Analysis of Fixed Immunocytochemically Identified Neuronal Cells

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Type: preprint

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Language: en

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Publication year: 2019

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Publication date: 2019-09-24

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Authors: Jaehee Lee, Youtao Lu, Jinchun Wang, Jifen Li, Stephen Fisher, C. Erik Nordgren, Jean G. Rosario, Stewart A. Anderson, Alexandra V. Ulyanova, Steven Brem, H. Isaac Chen, John A. Wolf, M. Sean Grady, Mimi Healy, Junhyong Kim, James Eberwine

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Landing page: https://doi.org/10.1101/780387

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Concepts: Chromatin, Biology, Cell biology, DNA, Single-cell analysis, ChIA-PET, Computational biology, Cell, Molecular biology, Genetics, Nucleosome

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