RT Journal
A1 Vahrenkamp, Jeffery M.
A1 Szczotka, Kathryn
A1 Dodson, Mark K.
A1 Jarboe, Elke A.
A1 Soisson, Andrew P.
A1 Gertz, Jason
T1 FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples
JF Genome Research 
JO Genome Research 
YR 2019 
FD November 01 
VO 29 
IS 11 
SP 1826 
OP 1835 
DO 10.1101/gr.249656.119 
UL http://genome.cshlp.org/content/29/11/1826.abstract 
AB The majority of clinical cancer specimens are preserved as formalin-fixed paraffin-embedded (FFPE) samples. For clinical molecular tests to have wide-reaching impact, they must be applicable to FFPE material. Accurate quantitative measurements of RNA derived from FFPE specimens is challenging because of low yields and high amounts of degradation. Here, we present FFPEcap-seq, a method specifically designed for sequencing capped 5′ ends of RNA derived from FFPE samples. FFPEcap-seq combines enzymatic enrichment of 5′ capped RNAs with template switching to create sequencing libraries. We find that FFPEcap-seq can faithfully capture mRNA expression levels in FFPE specimens while also detecting enhancer RNAs that arise from distal regulatory regions. FFPEcap-seq is a fast and straightforward method for making high-quality 5′ end RNA-seq libraries from FFPE-derived RNA.