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Table 3 Oligonucleotide primers used in the study

From: Optimized PCR conditions minimizing the formation of chimeric DNA molecules from MPRA plasmid libraries

Primer name

Sequence 5′ → 3′

Notes

Libr-A1-for

TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG TTCGGAGT GACACTCGAGGATCGAG

Illumina sequencing primer sites “seq1” and “seq2” are underlined by single and double lines, respectively.

Libr-A2-for

TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG ACTCATTT GACACTCGAGGATCGAG

Libr-A3-for

TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG GGGATCCG GACACTCGAGGATCGAG

The 8-bp sample index (“i”) sequences are in bold.

Libr-A5-for

TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG CAAGATAA GACACTCGAGGATCGAG

“Target specific forward” and “target specific reverse” sequences immediately flanking BC and ROI are in italic.

Libr-A6-for

TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG GGACAACG GACACTCGAGGATCGAG

Libr-A7-for

TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG AGCGAGCT GACACTCGAGGATCGAG

Libr-A8-for

TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG CTGCACGT GACACTCGAGGATCGAG

Libr-A9-for

TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG GCACTAGT GACACTCGAGGATCGAG

Libr-rev

GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG CCCTAGAAAGATAATCATATTGT

Libr-P5-for

AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTC

Illumina “P5” and “P7” adapters are underlined by single and double lines, respectively.

Libr-P7-rev

CAAGCAGAAGACGGCATACGAGATGTCTCGTGGGCTCGG

BC1

ACTAGGCAAGGCACCAG

 

BC2

CGAGGGATATAGAGCGAGTTAA

 

ROI1

TACGTTAAAGATAATCATGCATAAGTCG

 

ROI2

TACGTTAAAGATAATCATGCTATATGGC

 

Illumina-qPCR-1

AATGATACGGCGACCACCGA

KAPA Library Quantification Kit (Roche).

Illumina-qPCR-2

CAAGCAGAAGACGGCATACGA