Open AccessComparison of optimized methodologies for isolating nuclei from esophageal tissue
Author(s) -
Lucy Kimbley,
Rachel Parker,
Jack Harrington,
Robert C. Walker,
Ben Grace,
Jonathan West,
Tim Underwood,
Matthew Rose-Zerilli
Publication year - 2022
Publication title -
biotechniques/biotechniques
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.617
H-Index - 131
eISSN - 1940-9818
pISSN - 0736-6205
DOI - 10.2144/btn-2021-0036
Subject(s) - ribosome , rna , rnase p , ribosomal rna , gene , cell , microbiology and biotechnology , biology , computational biology , chemistry , genetics
Single-nuclei RNA sequencing allows single cell-based analysis in frozen tissue, ameliorating cell recovery biases associated with enzymatic dissociation methods. The authors present two optimized methods for isolating and sequencing nuclei from esophageal tissue using a commercial EZ and citric acid (CA)-based method. Despite high endogenous RNase activity, these protocols produced libraries of expected fragment length (average length EZ: 745 bp; CA: 1232 bp) with comparable complexity (median Transcript/Gene number, EZ: 496/254; CA: 483/256). CA nuclei showed a higher proportion of ribosomal gene reads, potentially reflecting co-isolation of nuclei and adherent ribosomes. The authors identified 11 cell lineages in the combined datasets, with differences in cell type recovery between the two methods, providing utility dependent on experimental needs.