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B.C.M. and B.W. performed targeted sequencing.
Targeting sequences were amplified using PCR protocols described by Yang et al., 2002), with minor modifications for different primers.
UOK262 cells (Yang et al., 2010b ) were transfected using FuGene6 (Roche) with either full length human FH (FH), or FH without the mitochondrial targeting sequence (FHcyt), following the manufacturer's protocol.
The protocols to generate constructs containing targeting sequences in pCRII-Topo vector and to produce dsRNA are described previously (Pile et al. 2002).
gRNA targeting sequences.
cperoxisome targeting sequence 1.
Our sequencing protocol is targeted at large genomes with chromosomes that are significantly longer than a clone length.
For library preparation of single samples, we followed the manufacturer's instructions (HaloPlex Target Enrichment System For Illumina Sequencing, Protocol version D, August 2012, Agilent Technologies, Santa Clara, CA, USA).
In this paper we have described SHRAP, a novel sequencing protocol and assembly methodology that targets future, high-throughput technologies that produce short reads.
Targeted sequencing was performed following the manufacturer's protocol (see Supplementary Methods).
Targeted sequencing was performed following the manufacturer's protocol on samples that passed QC parameters (see Supplementary Methods).
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