Raw Nanopore sequencing data of CD-pore-seq V1

=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 [e-mail], [e-mail] and [e-mail]

==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.

CD-pore-seq V1原始纳米孔测序数据

==作者==
Zicheng Yu¹, Zihao Chen¹, Thomas C. Williams¹,², Craig J. Anderson¹,³,⁴, Andrew P. Jackson¹,*, Martin A.M. Reijns¹,*, Martin S. Taylor¹,*¹ 英国爱丁堡大学遗传学与癌症研究所，医学研究理事会（MRC）人类遗传学研究室² 英国爱丁堡大学儿童生命与健康学院³ 德国海德堡德国癌症研究中心⁴ 德国慕尼黑德国癌症研究中心转化肿瘤学系

* 通讯作者邮箱：[e-mail]、[e-mail]及[e-mail]

==引用文献==
《基于纳米孔测序的DNA修饰检测通用训练方法》

==数据集说明==
本数据集包含用于训练机器学习模型以预测单DNA嵌入核糖核苷酸的文库纳米孔测序数据。
连接试剂盒：LSK-114（除ygDNA文库外均使用）或SQK-NBD114.96（仅ygDNA文库使用）
流动槽版本：R10.4.1
测序仪器：MinION 或 PromethION（仅./TelN/PromethION组适用）

==DRD64文库==
* 在MinION流动槽上测序单DNA嵌入核糖核苷酸DRD64文库，该文库包含64种脱氧核糖核苷酸-核糖核苷酸-脱氧核糖核苷酸序列背景的混合物。

==UMI文库==
* 在MinION流动槽上测序唯一分子标识符（UMI）文库（包含环绕单DNA嵌入核糖核苷酸的高复杂度随机序列），其第二条链由带有拆分式11nt UMI的引物合成。

==TelN文库==
* 在MinION流动槽（./MinION）或两台PromethION流动槽（PromethION）上测序TelN文库（包含环绕单DNA嵌入核糖核苷酸的高复杂度随机序列），该文库通过CD-pore-seq方法制备，其第二条链由带有TelN识别序列的引物合成，经TelN酶切后完成共价连接。

==ygDNA文库==
* 在MinION流动槽上测序混合酵母基因组DNA文库，使用ONT SQK-NBD114.96试剂盒进行条码标记（条码05：rnh201-缺失突变体；条码06：pol2-M644G + rnh201-缺失突变体；条码08：pol3-L612M + rnh201-缺失突变体）。

==混合修饰文库==
* 在MinION流动槽上测序通过CD-pore-seq方法制备的混合文库（带有掺入的条码序列标记），该文库包含7种位于特定核苷酸位置的DNA修饰类型，以及作为对照的4种经典DNA核苷酸（位于同一核苷酸位置）。

==无聚合酶CD-pore-seq文库==
* 在MinION流动槽上测序无聚合酶CD-pore-seq试点测试文库，该文库使用合成寡核苷酸制备。
* 直接连接三种杂交体：Adapter_USER、Adapter_TelN及测试寡核苷酸（摩尔比1:1:1）。
* 文库制备流程：地高辛（DIG）固定（使用Protein G磁珠（Dynabeads））→ USER酶切 → 生物素固定（使用Strep-M280磁珠（Dynabeads））→ TelN酶切 → T4多核苷酸激酶（T4-PNK）末端修复 → 接头连接。