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Table 1 Oligonucleotides

From: Application of nonsense-mediated primer exclusion (NOPE) for preparation of unique molecular barcoded libraries

Primer

Application

Sequence

Primers for linear PCR

EGFR-ex20_NNN

PCR-based introduction of UMI (UMI-containing primer), contains partial sequence of TruSeq Illumina adapter

ACACGACGCTCTTCCGATCTNNNNNNNNNNNNNNCATCTGCCTCACCTCCACCGT

EGFR-

ex18-1reg_NNN

ACACGACGCTCTTCCGATCTNNNNNNNNNNNNNNGAAGCTCCCAACCAAGCTC

EGFR-

ex19-1reg_NNN

ACACGACGCTCTTCCGATCTNNNNNNNNNNNNNNCTGTCATAGGGACTCTGGAT

EGFR

-ex21_R_NNN

ACACGACGCTCTTCCGATCTNNNNNNNNNNNNNNTCTTTCTCTTCCGCACCCAG

EGFR

-ex22_NNN

ACACGACGCTCTTCCGATCTNNNNNNNNNNNNNNCATCCCAAGGTGCCTATCAA

NOPE oligos

NOPE-R1

Neutralization of EGFR-ex20_NNN

GCACGCGTCGACGGTGGAGGTG-BHQ1

NOPE-R2

ACACGACGCTCTTCCGATCTACGGTGGAGGTGAGGCAG-BHQ1

NOPE-R3

GCACGCGTCGACGGTGGAGGTGAGGCAG-BHQ1

NOPE-R0

ACGGTGGAGGTGAGGCAG-BHQ1

NOPE-EGFR- ex18

Neutralization of EGFR-ex18-1reg_NNN

TCACACGTCTGAGCTTGGTTGGGAGCTTC-BHQ1

NOPE-EGFR-ex19

Neutralization of EGFR-

ex19-1reg_NNN

ATACTCTTCGATCCAGAGTCCCTATGACAG-BHQ1

NOPE- EGFR-ex21

Neutralization of EGFR-ex21_R_NNN

CTTGACGTCACTGGGTGCGGAAGAGAAAGA-BHQ1

NOPE- EGFR-ex22

Neutralization of EGFR-ex22_NNN

ACTCTCATCCTTGATAGGCACCTTGGGATG-BHQ1

Primers for the 1st PCR

EGFR-ex20_R1

Reverse nested EGFR-ex20-specific primer 1

TGTTCCCGGACATAGTCCAG

EGFR-ex18-1reg_ R1

Reverse nested EGFR-ex18-specific primer 1

AACGCACCGGAGCCCAGCACT

EGFR-ex19-1reg_R1

Reverse nested EGFR-ex19-specific primer 1

GATTTCCTTGTTGGCTTTCGGA

EGFR-ex21_F1

Forward nested EGFR-ex21-specific primer 1

CTGGTGAAAACACCGCAGCA

EGFR-ex22_R1

Reverse nested EGFR-ex22-specific primer 1

GCTCCAGACATCACTCTGGT

TruSeq-short

Step-out primer 1

TACACGACGCTCTTCCGATCT

Primers for 2nd PCR

EGFR-ex20_R2

Reverse nested EGFR-ex20-specific primer 2, contains partial sequence of TruSeq Illumina adapter

GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTACATAGTCCAGGAGGCAGC

EGFR-ex18-1reg_R2 Br

Reverse nested EGFR-ex18-specific primer 2, contains partial sequence of TruSeq Illumina adapter

GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCGGAGCCCAGCACTTTGATC

EGFR-ex19-1reg_R2 Br

Reverse nested EGFR-ex19-specific primer 2, contains partial sequence of TruSeq Illumina adapter

GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTGTTGGCTTTCGGAGATGTT

EGFR-ex21_F2 Br

Forward nested EGFR-ex21-specific primer 2, contains partial sequence of TruSeq Illumina adapter

GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAAACACCGCAGCATGTCAAG

EGFR-ex22_R2 Br

Reverse nested EGFR-ex22-specific primer 2, contains partial sequence of TruSeq Illumina adapter

GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTACATCACTCTGGTGGGTATAG

TruSeq-long

Step-out primer 2, contains sequence of TruSeq Illumina adapter

AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT

Primers for 3rd PCR (introducing Illumina indexes)

TruSeq-Index1

Reverse step-out primer, anneals on the EGFR-ex20_R2, contains complete sequence of TruSeq Illumina adapter with sample index

CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGT

Illumina-Dir

Forward step-out primer 3

AATGATACGGCGACCACCGAGATC

Real time PCR probes

Z-IGFR ex20

Real time PCR probe for exon 20.

Fam-AGCTCATCACGCAGCTCATGCCCTT-BHQ1

Z-TruUni

Universal real time PCR probe for TuSeq adapter

Fam-ACACTCTTTCCCTACACGACGCTCTT-BHQ1