Premium
Identifying and Correcting RNA Preservation Differences in Human Blood Samples
Author(s) -
Donohue Duncan,
Gautam Aarti,
AnnMiller Stacy,
Hammamieh Rasha,
Jett Marti
Publication year - 2015
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.29.1_supplement.562.20
Subject(s) - rna , computational biology , biology , genetics , gene
Different methods of mRNA preservation and handling can lead to differences in downstream analysis results. The specific effects on transcript degradation vary by sample handling and are difficult to predict a priori. Here, we compare duplicate blood samples from the same individuals collected in PaxGene, RNAGARD, and TRIzol tubes using Agilent whole genome arrays. Even with similar high RNA integrity number (RIN) values, we see strong systematic differences between the three methods of preservation, which may point to different degrees of transcription following sample collection. When comparing the ability of the three preservation methods to accurately separate individuals, RNAGard outperforms PaxGene, with both showing significantly better individual separation than TRIzol. Here we introduce a computational tool designed to identify and attempt to correct for RNA degradation and other preservation platform‐specific differences. Effects which cannot be accurately corrected will be flagged so that problematic probes or genes can be excluded from downstream analysis. Supported by USAMRMC grant NO: 09284002