Supplementary Data - Nanopore cDNA With and Without mtDNA

Update (v1.5.1-Demo): added 60Mb demonstration dataset for teaching / learning purposes. This dataset can be used for testing demultiplexing, or carrying out differential expression analysis on nanopore reads. There are 15k reads sampled from each run (subset on ~300 genes), plus 7.5k chimeric reads from the Dec17 run, plus 7.5k reads sampled from from CG009/BC08. The gene subset includes ~100 genes differentially-expressed between 4T1WT and 4T1ρ⁰ cell lines, plus an additional ~200 genes with minimal differential expression observed between any 4T1 cell lines (i.e. a housekeeping gene set): BC01, BC02, BC04, BC06 - 4T1 cell line reads from three sequencing runs (005, 005, 004, Dec17) BC03, BC05, BC07 - 4T1ρ⁰ (without mtDNA) cell line reads from three sequencing runs (005, 004, Dec17) BC08 - 4T1ρ⁰SC (from subcutaneous tumour) cell line reads from one sequencing run (009) Update (v1.5.0-Called): added full 4T1 call set (called using guppy high-accuracy v3.2.2), gene transcript count tables, and differential expression results Update (v1.4.1-Chimeric): added more example called chimeric reads of various [unclassified] categories Update (v1.4.0-Chimeric): added example chimeric reads, one formed [presumably] during sample prep ["conjugation"], another formed in-silico ["double read"] Update (v1.3.0-DESeq2): added count table and metadata file for DESeq2 analysis Update (v1.2.1-10k): added 10k of FASTQ reads from a more recent run (part of the same differential expression project). Supplementary data to go with David Eccles' poster about nanopore cDNA sequencing with and without mitochondrial DNA. Reference mouse mtDNA and mtDNA reads from 4T1 cells (from MinION cDNA sequencing, and from SRA run SRR6747859). fwd_4T1_BC06.correctedReads.uniqueOnly.fasta.gz -- Canu-corrected cDNA reads from Wildtype 4T1 strain, filtered as transcript-forward orientation rev_4T1_BC06.correctedReads.uniqueOnly.fasta.gz -- Canu-corrected cDNA reads from Wildtype 4T1 strain, filtered as transcript-reverse orientation fwd_4T1_BC07.correctedReads.uniqueOnly.fasta.gz -- Canu-corrected cDNA reads from 4T1ρ0 strain (no mitochondrial DNA), filtered as transcript-forward orientation rev_4T1_BC07.correctedReads.uniqueOnly.fasta.gz -- Canu-corrected cDNA reads from 4T1ρ0 strain (no mitochondrial DNA), filtered as transcript-reverse orientation Other intermediate data files are also included, see `4way_mapping_process.txt` for more details. The mpileup differential coverage script can be found here.更新（v1.5.1-Demo）：新增了60Mb的演示数据集，用于教学与学习用途。该数据集可用于测试解复用（demultiplexing），或针对纳米孔测序读段（nanopore reads）开展差异表达分析（differential expression analysis）。 每个测序批次均抽取了15k条读段（对应约300个基因的子集），此外还包含Dec17批次产生的7.5k条嵌合读段（chimeric reads），以及从CG009/BC08中抽取的7.5k条读段。该基因子集包含约100个在4T1野生型（4T1WT）与4T1ρ⁰（线粒体DNA缺失）细胞系间存在差异表达的基因，外加约200个在任意4T1细胞系间仅存在极微弱差异表达的基因（即持家基因集（housekeeping gene set））： BC01、BC02、BC04、BC06：来自4个测序批次（005、005、004、Dec17）的4T1细胞系读段 BC03、BC05、BC07：来自3个测序批次（005、004、Dec17）的4T1ρ⁰（线粒体DNA缺失）细胞系读段 BC08：来自1个测序批次（009）的4T1ρ⁰SC（皮下瘤来源）细胞系读段 更新（v1.5.0-Called）：新增了完整的4T1碱基识别结果集（使用Guppy（Guppy）高准确度v3.2.2版本进行碱基识别）、基因转录本计数表以及差异表达分析结果。 更新（v1.4.1-Chimeric）：新增了更多不同[未分类]类别的已识别嵌合读段示例。 更新（v1.4.0-Chimeric）：新增了嵌合读段示例，其中一条推测是在样本制备过程中形成的["结合"]，另一条为计算机模拟生成的["双读段（double read）"]。 更新（v1.3.0-DESeq2）：新增了用于DESeq2（DESeq2）差异表达分析的计数表与元数据文件。 更新（v1.2.1-10k）：新增了来自最新测序批次的10k条FASTQ（FASTQ）格式读段（属于同一差异表达分析项目的一部分）。 配套补充数据对应David Eccles关于携带与缺失线粒体DNA（mtDNA）的纳米孔cDNA测序的海报内容。包含参考小鼠线粒体DNA（mtDNA）以及4T1细胞的mtDNA读段（来自MinION（MinION）cDNA测序数据，以及SRA（Sequence Read Archive）序列号SRR6747859的测序数据）。 fwd_4T1_BC06.correctedReads.uniqueOnly.fasta.gz：来自野生型4T1菌株的Canu（Canu）校正cDNA读段，经筛选为转录本正向取向 rev_4T1_BC06.correctedReads.uniqueOnly.fasta.gz：来自野生型4T1菌株的Canu（Canu）校正cDNA读段，经筛选为转录本反向取向 fwd_4T1_BC07.correctedReads.uniqueOnly.fasta.gz：来自4T1ρ⁰（线粒体DNA缺失）菌株的Canu（Canu）校正cDNA读段，经筛选为转录本正向取向 rev_4T1_BC07.correctedReads.uniqueOnly.fasta.gz：来自4T1ρ⁰（线粒体DNA缺失）菌株的Canu（Canu）校正cDNA读段，经筛选为转录本反向取向 此外还包含其他中间数据文件，详细信息请参阅`4way_mapping_process.txt`。mpileup差异覆盖度分析脚本可在此处获取。