Extraction of RNA from formalin-fixed, paraffin-embedded equine placenta

Pouya Dini, Alejandro Esteller-Vico, Kirsten E. Scoggin, Peter Daels, Barry A. Ball

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

Abstract

Archived formalin-fixed, paraffin-embedded (FFPE) samples represent a valuable resource for the determination of gene expression for physio/pathological conditions. In the present study, we validated a protocol for the extraction of RNA from FFPE samples collected from healthy and diseased equine placenta. The quality and quantity of the extracted RNA from the FFPE and matching RNAlater™-preserved samples and expression levels of common housekeeping genes and reference microRNAs were evaluated. Precision of the expression data was evaluated by comparing relative expression of CYP19A1 and HSD3B1 in FFPE and RNAlater™ samples. The median RNA concentration recovered from FFPE samples was 316.8 ng/mm 3 of tissue (ranging between 61.6 and 917.4 ng/mm 3 ), average RNA integrity number was 2.3 ± 0.9 (mean ± standard deviation), and 84% of samples had RNA fragments longer than 200 nucleotides (DV 200 ). RNA concentrations and C T values for GAPDH, ACTB, miR-8908a and miR-369 in FFPE samples were significantly correlated (r = −0.8, −0.7, −0.4 and −0.4, respectively; p < 0.001). Expression pattern of normalized CYP19A1 and HSD3B1 in paired FFPE and RNAlater™ samples was significantly correlated (r = 0.97 for CYP19A1 and HSD3B1; p < 0.001). This study demonstrates that RNA can be extracted from FFPE equine placental tissue and used for downstream transcriptomic analysis. Similar RNA expression patterns were obtained using RNAlater™ and FFPE tissue samples.

Original languageEnglish
Pages (from-to)627-634
Number of pages8
JournalReproduction in Domestic Animals
Volume54
Issue number3
DOIs
StatePublished - Mar 2019

Bibliographical note

Publisher Copyright:
© 2019 Blackwell Verlag GmbH

Keywords

  • RNA extraction
  • equine
  • formalin-fixed
  • paraffin-embedded
  • placenta
  • placentitis
  • pregnancy

ASJC Scopus subject areas

  • Biotechnology
  • Animal Science and Zoology
  • Endocrinology

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