Raw Nanopore sequencing data of CD-pore-seq V1
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=Raw Nanopore sequencing data of CD-pore-seq V1= ==Author==Zicheng Yu1, Zihao Chen1, Thomas C. Williams1,2, Craig J. Anderson1,3,4, Andrew P. Jackson1,*, Martin A.M. Reijns1,*, Martin S. Taylor1,*1 MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, UK.2 Child Life and Health, University of Edinburgh, UK.3 German Cancer Research Center, Heidelberg, Germany4 Department of Translational Oncology, German Cancer Research Center, Munich, Germany. * Correspondence should be addressed to andrew.jackson@ed.ac.uk, martin.reijns@ed.ac.uk and martin.taylor@ed.ac.uk ==Citation=='Generalised training for DNA modification detection by nanopore sequencing' ==Description==Nanopore sequencing data of libraries to train machine learning models to predict single DNA-embedded ribonucleotides.Ligation kit: LSK-114 (all except for ygDNA) or SQK-NBD114.96 (ygDNA)Flow-cell version: R10.4.1Sequencing device: MinION or PromethION (./TelN/PromethION only) ==DRD64==* Sequencing the single DNA-embedded ribonucleotide DRD64 library on a MinION flow-cell, a mixture of 64 types of deoxyribonucleotide-ribonucleotide-deoxyribonucleotide context. ==UMI==* Sequencing the UMI library (high-complexity randomers surrounding single DNA-embedded ribonucleotides) on a MinION flow-cell, with the second strand synthesised by the primer containing split 11nt UMIs. ==TelN==* Sequencing the TelN library (high-complexity randomers surrounding single DNA-embedded ribonucleotides) on a MinION flow-cell (./MinION) or two PromethION flow-cells (PromethION), prepared by CD-pore-seq (with the second strand synthesised by the primer containing TelN recognition sequence, cut and covalently linked by TelN digestion). ==ygDNA==* Sequencing a pooled yeast gDNA libary on a MinION flow-cell, barcoded using ONT SQK-NBD114.96 kit (barcode05:rnh201-null; barcode06:pol2-M644G+rnh201-null; barcode08: pol3-L612M+rnh201-null). ==Mixed_Modifications==* Sequencing a mixed (barcoded with incorporated barcode sequences) library prepared by CD-pore-seq on a MinION flow-cell, containing 7 types of DNA modifications at a defined nucleotide position, and 4 canonical DNA nucleotides at the same position as the control. ==pol-free_CD_pore_seq==* Sequencing a pilot testing library on a MinION flow-cell, prepared by polymerase-free CD-pore-seq using synthetic oligos.* Directly ligation of three hybrids: Adapter_USER; Adapter_TelN; test oligo (1:1:1).* Library preparation: DIG-immobilisation using protein-G dynabeads -> USER digestion -> Biotin-immobilisation using strep-M280 dynabeads -> TelN digestion -> T4-PNK end-prep -> Adapter Ligation.
