Low-input ATAC&mRNA-seq protocol for simultaneous profiling of chromatin accessibility and gene expression

Low-input ATAC&mRNA-seq protocol for simultaneous profiling of chromatin accessibility and gene expression

Summary: We present a simple, fast, and robust protocol (low-input ATAC&mRNA-seq) to simultaneously generate ATAC-seq and mRNA-seq libraries from the same cells in limited cell numbers by coupling a simplified ATAC procedure using whole cells with a novel mRNA-seq approach that features a seamle...

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Bibliographic Details
Main Authors: Ruifang Li, Sara A. Grimm, Paul A. Wade
Format: Article
Language:English
Published: Elsevier 2021-09-01
Series:STAR Protocols
Subjects:
Genomics
High Throughput Screening
Molecular Biology
Online Access:http://www.sciencedirect.com/science/article/pii/S2666166721004706
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spelling doaj-ee7dedd7fb3c42058a53d13a20146f3d2021-09-19T05:01:05ZengElsevierSTAR Protocols2666-16672021-09-0123100764Low-input ATAC&mRNA-seq protocol for simultaneous profiling of chromatin accessibility and gene expressionRuifang Li0Sara A. Grimm1Paul A. Wade2Epigenetics Innovation Lab, Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Corresponding authorIntegrative Bioinformatics Support Group, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USAEukaryotic Transcriptional Regulation Group, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USASummary: We present a simple, fast, and robust protocol (low-input ATAC&mRNA-seq) to simultaneously generate ATAC-seq and mRNA-seq libraries from the same cells in limited cell numbers by coupling a simplified ATAC procedure using whole cells with a novel mRNA-seq approach that features a seamless on-bead process including direct mRNA isolation from the cell lysate, solid-phase cDNA synthesis, and direct tagmentation of mRNA/cDNA hybrids for library preparation. It enables dual-omics profiling from limited material when joint epigenome and transcriptome analyses are needed.For complete details on the use and execution of this protocol, please refer to Li et al. (2021).http://www.sciencedirect.com/science/article/pii/S2666166721004706GenomicsHigh Throughput ScreeningMolecular Biology
collection DOAJ
language English
format Article
sources DOAJ
author Ruifang Li
Sara A. Grimm
Paul A. Wade
spellingShingle Ruifang Li
Sara A. Grimm
Paul A. Wade
Low-input ATAC&mRNA-seq protocol for simultaneous profiling of chromatin accessibility and gene expression
STAR Protocols
Genomics
High Throughput Screening
Molecular Biology
author_facet Ruifang Li
Sara A. Grimm
Paul A. Wade
author_sort Ruifang Li
title Low-input ATAC&mRNA-seq protocol for simultaneous profiling of chromatin accessibility and gene expression
title_short Low-input ATAC&mRNA-seq protocol for simultaneous profiling of chromatin accessibility and gene expression
title_full Low-input ATAC&mRNA-seq protocol for simultaneous profiling of chromatin accessibility and gene expression
title_fullStr Low-input ATAC&mRNA-seq protocol for simultaneous profiling of chromatin accessibility and gene expression
title_full_unstemmed Low-input ATAC&mRNA-seq protocol for simultaneous profiling of chromatin accessibility and gene expression
title_sort low-input atac&mrna-seq protocol for simultaneous profiling of chromatin accessibility and gene expression
publisher Elsevier
series STAR Protocols
issn 2666-1667
publishDate 2021-09-01
description Summary: We present a simple, fast, and robust protocol (low-input ATAC&mRNA-seq) to simultaneously generate ATAC-seq and mRNA-seq libraries from the same cells in limited cell numbers by coupling a simplified ATAC procedure using whole cells with a novel mRNA-seq approach that features a seamless on-bead process including direct mRNA isolation from the cell lysate, solid-phase cDNA synthesis, and direct tagmentation of mRNA/cDNA hybrids for library preparation. It enables dual-omics profiling from limited material when joint epigenome and transcriptome analyses are needed.For complete details on the use and execution of this protocol, please refer to Li et al. (2021).
topic Genomics
High Throughput Screening
Molecular Biology
url http://www.sciencedirect.com/science/article/pii/S2666166721004706
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AT saraagrimm lowinputatacmrnaseqprotocolforsimultaneousprofilingofchromatinaccessibilityandgeneexpression
AT paulawade lowinputatacmrnaseqprotocolforsimultaneousprofilingofchromatinaccessibilityandgeneexpression
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