@inbook{ff03575fac2c4b4d84a8450724b62953,
title = "In Vivo Genome-Wide RNA Structure Probing with Structure-seq",
abstract = "In vivo genome-wide RNA structure probing provides a global view of RNA structure as it occurs in the cell and can assist in elucidating important functional aspects of RNA structure. Structure-seq2 provides high-quality data on transcriptome-wide RNA structure in vivo but contains numerous steps that require technical precision. In this chapter we present the steps needed to produce high-quality structural data with a focus on controls and troubleshooting. Structure-seq2 can be applied to numerous organisms including plants, humans, and bacteria and is amenable to a wide variety of RNA-modifying chemicals including DMS, glyoxal, and SHAPE reagents. Notably, the data generated by the method highlighted here can be readily analyzed using our StructureFold2 computational pipeline.",
author = "Ritchey, {Laura E.} and Zhao Su and Assmann, {Sarah M.} and Bevilacqua, {Philip C.}",
note = "Funding Information: We thank Dr. David Mitchell and Dr. Joseph Waldron for helpful input on the manuscript and Dr. Craig Praul (Genomics Core Facility, Penn State University) for high-throughput Illumina sequencing. This work was supported by the National Science Foundation Plant Genome Research Program (NSF-IOS-1339282), with additional support from an Innovation Award from Penn State University.",
year = "2019",
doi = "10.1007/978-1-4939-9045-0_20",
language = "English (US)",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "305--341",
booktitle = "Methods in Molecular Biology",
}