Abstract: Objective · To compare the quality of RNA extracted fresh and formalin-fixed paraffin-embedded (FFPE) brain tissues and to explore the long non-coding RNA (lncRNA) level. Methods · FFPE samples stored under various conditions and paired frozen brain tissues were collected and total RNA qualities were then detected. Amplification efficiency (AE) and stability of each RNA marker were calculated and analyzed based on real-time quantitative PCR. After selecting reference biomarkers, normalized △Ct values of candidate makers within different amplicon size were measured to assess the possibility of lncRNA quantification in FFPE tissues. Results · The purity of RNA extracted FFPE was relatively high, but the RNA integrity was lower than fresh samples. All biomarkers were successfully amplified and amplification efficiencies of long-chain RNA markers were correlated with amplicon sizes, sample treatment and preservation conditions, namely temperature and storage time. 5S, miR-9 and miR-125bachieved optimal AE and showed quite s in all specimens, therefore they were chosen as control markers. Compared with fresh samples, the △Ct values of only 2 lncRNA (HAR1F and MALAT1-L, whose amplicon size were both higher than 200 bp, respectively) increased in the FFPE samples kept in 4 ℃, while in FFPE tissues kept in room temperature, increments of the △Ct values were significant for most target genes except for short amplicon markers (<60 bp), which showed consistently s in all brain specimens. Conclusion · RNA integrity is affectedsample treatment and preservation conditions, but lncRNA levels in FFPE tissues can be accurately quantificatedusing optimal amplicon sizes and considerable reference markers.

Key words: brain tissue, formalin-fixed paraffin-embedded, RNA, quality, amplification efficiency, internal reference marker, long non-coding RNA