Table 1.

Primers and sample keys (bar codes are underlined). NlaIII sites in SWITCH primers are boxed while TaiI sites are double underlined.

List of oligonucleotides used for PAT preparation
Designation	Sequence (5’ -> 3’)	Use
Primers used for Method 1
RT-PE1 series	5’-biotin–TCCTGCTGAACCGCTCTTCCGATCTNNNXXTTTTTTTTTTTTTTTTTTVN	Reverse transcription primer
RT-PE2 series	TCCTGCTGAACCGCTCTTCCGATCTNNNXXTTTTTTTTTTTTTTTTTTVN	Reverse transcription primer
PE-RTbio	5’-biotin TCCTGCTGAACCGCTCTTCCGATCT	Second strand synthesis
SWITCH1.1		Strand switching
SWITCH1.2		Second strand synthesis
PE-ADN1A		Ligation of 5’ Illumina adapter
PE-ADT1A		Ligation of 5’ Illumina adapter
PE-AD2A	AGATCGGAAGAGCGTCGTGTAGTCTGTCGAGAC	Ligation of 5’ Illumina adapter
PE-ADN1B		Ligation of 5’ Illumina adapter
PE-ADT1B		Ligation of 5’ Illumina adapter
PE-AD2B	TCAGATCGGAAGAGCGTCGTGTAGTCTGTCGAGAC	Ligation of 5’ Illumina adapter
PE-ADN1C		Ligation of 5’ Illumina adapter
PE-ADT1C		Ligation of 5’ Illumina adapter
PE-AD2C	AGAGATCGGAAGAGCGTCGTGTAGTCTGTCGAGAC	Ligation of 5’ Illumina adapter
PE-ADN1D		Ligation of 5’ Illumina adapter
PE-ADT1D		Ligation of 5’ Illumina adapter
PE-AD2D	GGAGATCGGAAGAGCGTCGTGTAGTCTGTCGAGAC	Ligation of 5’ Illumina adapter
Primers used for Methods 2A and 2B
RT-PE3 series	ACACTCTTTCCCTACACGACGCTCTTCCGATCTNNXXXTTTTTTTTTTTTTTTTTTVN	Reverse transcription primer
SWITCH2	CGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGGG	Strand switching
Primers used to amplify tags
PE-PCR1	AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT	Tag amplification
PE-PCR2	CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT	Tag amplification

“N” – random base

“V” – A, C, or G, randomized in the primer population

“XX”, “XXX” – positions of bar codes used to distinguish samples for multiplex sequencing.