title: miRNA in situ hybridization in formaldehyde and EDC-fixed tissues.
abstract: MicroRNAs are small regulatory RNAs with many biological functions and disease associations. We showed that in situ hybridization (ISH) using conventional formaldehyde fixation results in substantial microRNA loss from mouse tissue sections, which can be prevented by fixation with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide that irreversibly immobilizes the microRNA at its 5' phosphate. We determined optimal hybridization parameters for 130 locked nucleic acid probes by recording nucleic acid melting temperature during ISH.
authors.affiliation: Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, New York 10065, USA.
authors.forename: John T G
authors.initials: JT
authors.lastname: Pena
authors.forename: Cherin
authors.initials: C
authors.lastname: Sohn-Lee
authors.forename: Sara H
authors.initials: SH
authors.lastname: Rouhanifard
authors.forename: Janos
authors.initials: J
authors.lastname: Ludwig
authors.forename: Markus
authors.initials: M
authors.lastname: Hafner
authors.forename: Aleksandra
authors.initials: A
authors.lastname: Mihailovic
authors.forename: Cindy
authors.initials: C
authors.lastname: Lim
authors.forename: Daniel
authors.initials: D
authors.lastname: Holoch
authors.forename: Philipp
authors.initials: P
authors.lastname: Berninger
authors.forename: Mihaela
authors.initials: M
authors.lastname: Zavolan
authors.forename: Thomas
authors.initials: T
authors.lastname: Tuschl
mesh_terms: D000818:Animals; D001921:Brain / Q000166:cytology / Q000378:metabolism; D001923:Brain Chemistry; D002234:Carbodiimides / Q000737:chemistry*; D005557:Formaldehyde / Q000737:chemistry*; D017403:In Situ Hybridization / Q000379:methods*; D051379:Mice; D035683:MicroRNAs / Q000032:analysis* / Q000235:genetics; D008856:Microscopy, Fluorescence / Q000379:methods; D009474:Neurons / Q000166:cytology / Q000378:metabolism; D016707:Tissue Fixation / Q000379:methods*
chemical_list: C518491:1-ethyl-3-(3-(diethylamino)propyl)carbodiimide; D002234:Carbodiimides; D035683:MicroRNAs; D005557:Formaldehyde