. Author manuscript; available in PMC: 2015 Jan 1.

Published in final edited form as: Nat Protoc. 2014 Jun 26;9(7):1740–1759. doi: 10.1038/nprot.2014.121

Table 1.

Used oligonucleotides.

5RNAGsuI	CACTCTrGrArGrCrArArUrArCrC
PET-3RT-A	ACATGTATAGCGGCCGCTAGANNNNNNNVTTTTTTTTTTTTTTTTVN
PET-3RT-B	ACATGTATAGCGGCCGCATCTNNNNNNNVTTTTTTTTTTTTTTTTVN
PET-5ABio	TATAGCGGCCGCAC[BtndT]GCACTCTGAGCAATACC
PET-5BBio	TATAGCGGCCGCTGA[BtndT]CACTCTGAGCAATACC
PET-5A	TATAGCGGCCGCACTGCACTCTGAGCAATACC
PET-5B	TATAGCGGCCGCTGATCACTCTGAGCAATACC
PET-3-A	ACATGTATAGCGGCCGCTAGA
PET-3-B	ACATGTATAGCGGCCGCATCT
Barcoded forked adaptors^#
mp1PE1	[Phos]AGCGCTAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
mp1PE2	ACACTCTTTCCCTACACGACGCTCTTCCGATCTAGCGCT^* T
mp5PE1	[Phos]ACAGTGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
mp5PE2	ACACTCTTTCCCTACACGACGCTCTTCCGATCTCACTGT^* T
mp19PE1	[Phos]CGGAATAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
mp19PE2	ACACTCTTTCCCTACACGACGCTCTTCCGATCTATTCCG^* T
mp22PE1	[Phos]CTATACAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
mp22PE2	ACACTCTTTCCCTACACGACGCTCTTCCGATCTGTATAG^* T
mp34PE1	[Phos]GGTAGCAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
mp34PE2	ACACTCTTTCCCTACACGACGCTCTTCCGATCTGCTACC^* T
mp37PE1	[Phos]GTTTCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
mp37PE2	ACACTCTTTCCCTACACGACGCTCTTCCGATCTCGAAAC^* T

All oligos are HPLC purified. [BtndT] refers to Biotin dT; [Phos] refers to 5′ Phosphorylation; bases precede by “r” refer to ribonucleotides;

refers to S-linkage between the two bases. Random barcodes are identified in bold, 3′ and 5′ chimera barcodes are underlined and NotI recognition sequence in italics. Sequences are represented in 5′ to 3′orientation.