TY - JOUR
T1 - Quality control and evaluation of plant epigenomics data
AU - Schmitz, Robert J.
AU - Marand, Alexandre P.
AU - Zhang, Xuan
AU - Mosher, Rebecca A.
AU - Turck, Franziska
AU - Chen, Xuemei
AU - Axtell, Michael J.
AU - Zhong, Xuehua
AU - Brady, Siobhan M.
AU - Megraw, Molly
AU - Meyers, Blake C.
N1 - Funding Information: This commentary was funded with support from the National Science Foundation (NSF IOS-1856627 and MCB-1856143) and the National Institutes of Health (NIH R01GM134682) to R.J.S., an NSF Postdoctoral Fellowship in Biology (DBI-1905869) to A.P.M., and NSF (MCB-1552455 and MCB-2043544) and NIH (R35GM124806) grants to X.Z. Publisher Copyright: © The Author(s) 2021. Published by Oxford University Press on behalf of American Society of Plant Biologists.
PY - 2022/1
Y1 - 2022/1
N2 - Epigenomics is the study of molecular signatures associated with discrete regions within genomes, many of which are important for a wide range of nuclear processes. The ability to profile the epigenomic landscape associated with genes, repetitive regions, transposons, transcription, differential expression, cis-regulatory elements, and 3D chromatin interactions has vastly improved our understanding of plant genomes. However, many epigenomic and single-cell genomic assays are challenging to perform in plants, leading to a wide range of data quality issues; thus, the data require rigorous evaluation prior to downstream analyses and interpretation. In this commentary, we provide considerations for the evaluation of plant epigenomics and single-cell genomics data quality with the aim of improving the quality and utility of studies using those data across diverse plant species.
AB - Epigenomics is the study of molecular signatures associated with discrete regions within genomes, many of which are important for a wide range of nuclear processes. The ability to profile the epigenomic landscape associated with genes, repetitive regions, transposons, transcription, differential expression, cis-regulatory elements, and 3D chromatin interactions has vastly improved our understanding of plant genomes. However, many epigenomic and single-cell genomic assays are challenging to perform in plants, leading to a wide range of data quality issues; thus, the data require rigorous evaluation prior to downstream analyses and interpretation. In this commentary, we provide considerations for the evaluation of plant epigenomics and single-cell genomics data quality with the aim of improving the quality and utility of studies using those data across diverse plant species.
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U2 - 10.1093/plcell/koab255
DO - 10.1093/plcell/koab255
M3 - Article
C2 - 34648025
SN - 1040-4651
VL - 34
SP - 503
EP - 513
JO - Plant Cell
JF - Plant Cell
IS - 1
ER -