GSM5462969: pIXHALO_PN94-B_r1; Vitis vinifera; OTHER
Genomic DNA was extracted following procedure described in Chin et al., 2016 (Chin, CS., Peluso, P., Sedlazeck, F. et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods 13, 1050–1054 (2016). https://doi.org/10.1038/nmeth.4035). DAP-seq experiment was performed as described in Bartlett et al., 2017 (Bartlett, A., O'Malley, RC., Huang, SC. et al. Mapping genome-wide transcription-factor binding sites using DAP-seq. Nat Protoc 12:1659-1672 (2017). https://doi.org/10.1038/nprot.2017.055).  The DAP-Seq DNA library is prepared from fragmented naked genomic DNA ligated with a short DNA sequence (20bp) encoding a truncated Illumina TruSeq adapter.  Separately, a construct containing a HALO-tagged transcription factor is translated by in vitro (rabbit reticulocyte) expression system. The affinity-tagged protein is immobilized on the appropriate affinity resin.  The DNA affinity purification step begins by combining the DNA library with the immobilized transcription factor. After the wash steps remove the unbound DNA, the bound DNA fraction is eluted. The eluted DNA fragments are PCR amplified with a full-length indexed TruSeq primer and directly sequenced on the Illumina NextSeq 500. DAP-Seq