Paraffin embedding contributes to RNA aggregation, reduced RNA yield, and low RNA quality.

ABSTRACT: The RNA isolated from FFPE tissues is of poor quality and quantity. Other studies have indicated that formaldehyde fixation or the duration of storage of tissue blocks accounted for RNA damage. Herein we report a third source of harm to RNA: embedding in warm paraffin. RNA bound to oligo(dT)-conjugated magnetic beads (an mRNA model) and total cellular RNA pellets were passed through formalin, graded ethanols, xylene, paraffin, and a formaldehyde demodification step. The mRNA model yielded at least 1550 bp amplicons at RT-PCR at each step of processing except paraffin, which yielded no more than 750 bp amplicons regardless of paraffin formulation or transition solvent. Quantitative RT-PCR on paraffinized RNA suggested a 1400-fold or more decrease in amplifiable RNA when compared with contro

SUBMITTER: Evers DL 

PROVIDER: S-EPMC3194049 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature