TY  - JOUR
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
Y1  - 2019/11/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1826 
EP  - 1835 
DO  - 10.1101/gr.249656.119 
VL  - 29 
IS  - 11 
UR  - http://genome.cshlp.org/content/29/11/1826.abstract 
N2  - 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. 
ER  -