title: Purification of high-quality RNA from synthetic polyethylene glycol-based hydrogels.
abstract: Polyethylene glycol (PEG)-based hydrogels, with variable stiffness, are widely used in tissue engineering to investigate substrate stiffness effects on cell properties. Transcriptome analysis is a critical method for understanding cell physiology. However, significant RNA degradation was observed during the process of isolating and purifying RNA from cells encapsulated in the PEG hydrogel, thereby precluding purification of high-quality RNA. Here, we describe a simple protocol that prevents RNA degradation and improves the quality and yield of RNA isolated from cells cultured in PEG hydrogels. This modification produces high-quality total RNA suitable for RNA sequencing and microarray analysis.
authors.affiliation: Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Gasparian
authors.affiliation: Department of Chemical Engineering, College of Engineering and Computing, University of South Carolina, Columbia, SC 29208, USA.
authors.forename: Leily
authors.initials: L
authors.lastname: Daneshian
authors.affiliation: Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA.
authors.forename: Hao
authors.initials: H
authors.lastname: Ji
authors.affiliation: Department of Chemical Engineering, College of Engineering and Computing, University of South Carolina, Columbia, SC 29208, USA. Electronic address: jabbari@cec.sc.edu.
authors.forename: Esmaiel
authors.initials: E
authors.lastname: Jabbari
authors.affiliation: Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA. Electronic address: shtutmanm@sccp.sc.edu.
authors.forename: Michael
authors.initials: M
authors.lastname: Shtutman
mesh_terms: D002478:Cells, Cultured; D005591:Chemical Fractionation / Q000379:methods*; D020100:Hydrogels / Q000737:chemistry*; D011092:Polyethylene Glycols / Q000737:chemistry* / Q000494:pharmacology; D011786:Quality Control; D012313:RNA / Q000737:chemistry / Q000302:isolation & purification*; D020871:RNA Stability
chemical_list: D020100:Hydrogels; D011092:Polyethylene Glycols; D012313:RNA
keywords: PEG hydrogel; RNA; RNA integrity; RNA purification; RNA-seq