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. 2019 Mar 22;212(1):153–174. doi: 10.1534/genetics.119.302058

Table 5. Oligonucleotides used for ChIP.

Primer Sequence
NRD1-5′-ChIP-F 5′-AGGGCAAGTGTTTCGTCC-3′
NRD1-5′-ChIP-R 5′-AAACTCGTAAAGGGAAGGAGC-3′
NRD1-5′-ChIP-probe /56-FAM/CCTCCATGT/ZEN/TCCATTCCTCGTTAGCA/3IABkFQ/
PCF11-5′-ChIP-F 5′-ATTGGATGAGAACTTGGCCT-3′
PCF11-5′-ChIP-R 5′-CTCCGAAAATTGTCCTGGTAATTC-3′
PCF11-5′-ChIP-probe /56-FAM/TTTGAAATT/ZEN/TCGCTTTCTTCCCATGCCT/3IABkFQ/
YOP1-ORF-ChIP-F (1) 5′-GGTTTTATTGGTTCCATCGTCATC-3′
YOP1-ORF-ChIP-R (1) 5′-CTTTCTTGTTAGTATAACTGCTTCGG-3′
YOP1-ORF-ChIP-probe (1) /56-FAM/TGTGTCGGG/Zen/TCATTTGGCTGTTTG/3IABkFQ/
YOP1-3′UTR-ChIP-F (2) 5′-AGACAGAAAAGGATGAAATTAGAGC-3′
YOP1-3′UTR-ChIP-R (2) 5′-TTTGAGGATATAGGTGAGTTGCC-3′
YOP1-3′UTR-ChIP-probe (2) /56-FAM/CTGTAGCCT/ZEN/TAGAAGCCTCATTGACGG/3IABkFQ/
YOP1-readthrough-ChIP-F (3) 5′-TTGGAGTCGTTTATGGTGTCC-3′
YOP1-readthrough-ChIP-R (3) 5′-TCTGTCGCGCATATCAAGAG-3′
YOP1-readthrough-ChIP-probe (3) /56-FAM/TCATCGTGT/Zen/TGTGTCGTGACGTGT/3IABkFQ/
RBG1-ORF-ChIP-F (1) 5′-CCAAAAGAACAAGGCCACATC-3′
RBG1-ORF-ChIP-R (1) 5′-GCCACATCAAAACCAATACCAG-3′
RBG1-ORF-ChIP-probe (1) /56-FAM/TGGGTCAAC/Zen/TGAAGGCCAAGCTG/3IABkFQ/
RBG1-readthrough-ChIP-F (3) 5′-CTACCGAGGGCTCTTCAAAAG-3′
RBG1-readthrough-ChIP-R (3) 5′-AGATGTGTCAATTTACCAGAAAACTC-3′
RBG1-readthrough-ChIP-probe (3) /56-FAM/CGACCTCGC/Zen/TTTGTGGTACCCAT/3IABkFQ/
YNL190W- ORF-ChIP-F (1) 5′-CTATTACTCTAGCCACCGTTGC-3′
YNL190W- ORF-ChIP-R (1) 5′-AACTACCGTCCGATGACAAAG-3′
YNL190W- ORF-ChIP-probe (1) /56-FAM/TGCCACTGC/Zen/TAAGAAGGGTGAACAT/3IABkFQ/
YNL190W-3′UTR-ChIP-F (2) 5′-GGAAGACCTAATTTTCTCCGGT-3′
YNL190W-3′UTR-ChIP-R (2) 5′-CACAAGCACACGTAAACACATAG-3′
YNL190W-3′UTR-ChIP-probe (2) /56-FAM/TCAGGATGA/ZEN/AGGGGGTAGGGGG/3IABkFQ/
YNL190W-readthrough-ChIP-F (3) 5′-GAGAAAGATCATCCAACTTTTAATCATG-3′
YNL190W-readthrough-ChIP-R 5′-AGCGTAGAAATAAGGAAAAAGAGAAAG-3′
YNL190W-readthrough-ChIP-probe /56-FAM/CGAATGTGG/ZEN/AAGGAAAATAGAGCGGAGC/3IABkFQ/

Oligos correspond to Figure 2 and Figure 4. Numbers in parentheses correspond to the primer sets used in Figure 4C & D.