. Author manuscript; available in PMC: 2019 May 13.

Published in final edited form as: Nat Protoc. 2018 Nov;13(11):2615–2642. doi: 10.1038/s41596-018-0055-0

TABLE 2 |.

Primers, probes and adapter sequences

Primer	Sequence (5’-3’)	Purpose
sgRNA-top	ATAGNNNNNNNNNNNNNNNNNNNN	Clone sgRNA into pCRL1 or equivalent vector (Step 9 (B))
sgRNA-bottom	AAACNNNNNNNNNNNNNNNNNNNN	Clone sgRNA into pCRL1 or equivalent vector (Step 9 (B))
M13 Reverse	CAGGAAACAGCTATGAC	Sequencing sgRNA cloned into pCRL1 (Step 9 (B, xii))
oSQT1143	GGAGCAGCTGGTCAGAGGGG	Amplify example EMX1 locus²⁶ (Step 10)
oSQT1144	GGGAAGGGGGACACTGGGGA	Amplify example EMX1 locus²⁶ (Step 10)
oSQT1288	/5Phos/CGGTGGACCGATGATC /ideoxyU/ ATCGGTCCACCG^*T	CIRCLE-seq hairpin adapter (Step 27)
oSQT1274	AATGATACGGCGACCACCGAG	TruSeq F1 (Step 79)
oSQT1275	CAAGCAGAAGACGGCATACGAGAT	TruSeq R1 (Step 79)
oSQT1310	/56-FAM/CCTACACGA/ZEN/CGCTCTTCCGATCT/3IABkFQ/	TruSeq probe (Step 79)
oSQT1311	/5HEX/TCGGAAGAG/ZEN/CACACGTCTGAACT/3IABkFQ/	TruSeq probe

indicates phosphorothioate linkage.

/5Phos/ indicates 5’ phosphorylation.

/ideoxyU/ indicates internal deoxyUridine

/56-FAM/ indicates 5’ fluorescein modification

/5HEX/ / indicates 5’ hexachlorofluorescein modification

/ZEN/ and /3IABkFQ/ are non-fluorescent quenchers.