Processed unique sort BAM files of High Risk HPV types 16, 18, 45 and 68b transcripts

RNAseq raw data of RNA extracted from five cervical cancer cell lines were mapped to HPV16 (NC_001526.2 or NC_001526.4), HPV18 (NC_001357.1), HPV68b (FR751039.1) and HPV45 (X74479.1). The processed BAM files were further analysed using The Hisat2 v2.1.0 aligner, Cufflinks v. 2.2.1, Cuffmerge and Cuffdiff. The processed sort BAM files containing sequences of viral transcripts were shown as ‘sort BAM files’. The HPV16 transcripts data and their expression levels reported as FPKM can be visualized using IGV software. The number of total reads and viral reads after mapping to viral references were shown in ‘HR-HPV genes and isoforms FPKM tracking file’, the spliced transcripts were named as CUFF. The integration sites of four high risk HPV types were analysed and shown in ‘fusion file’. According to IGV visualization, the splicing junctions of all four HPV types were found within E6 and E1 regions. For E6 region, one splicing donor (SD) at the 5′ end and different splicing acceptor (SA) positions at the 3′ end were found as follow; three splicing junctions were found in HPV16 positive cervical cancer cell lines, CaSki and SiHa, SD226^SA409(E6*I), SD226^SA526(E6*II) and SD226^SA742(E6*X). Two splicing junctions were found in HPV18 (HeLa), SD233^SA416(E6*I), SD233^SA635, HPV45(MS751); SD230^SA412(E6*I), SD230^SA640 and HPV68b (ME180); SD129^SA311(E6*I), SD129^SA406. Splicing junctions within E1 region found in CaSki and SiHa were SD880^SA3358, SD880^SA3361, SD880^SA3391, SD880^SA1726, SD880^SA2405, SD880^SA2582(E1C), SD880^SA2709(E2*), SD880^SA3020, SD880^SA3078, SD880^SA3329, SD577^SA6810, SD898^SA1725, SD1302^SA2709, SD1302^SA3358(E2C), SD1760^SA3391, SD1263^SA3391, SD2309^SA3461 and the other forms were SD96^SA1063, SD226^SA2709 (E6*IV), SD226^SA3329, SD226^SA3358(E6*III), SD226^SA3361, SD226^SA3391 and SD579^SA6809. Splicing junctions within E1 region in HPV18(HeLa) were SD929^SA2779, SD977^SA1836, SD1342^SA1436, SD1987^SA2047 and one splicing event within E7 region, SD599^SA619. HPV68b(ME180) were SD839^SA2586, SD683^SA2586, SD839^SA2586 and no E1 splicing junctions were found in HPV45(MS751).从5株宫颈癌细胞系中提取的RNA的RNA测序（RNAseq）原始数据，被比对至人乳头瘤病毒（Human Papillomavirus, HPV）16型（登录号NC_001526.2或NC_001526.4）、HPV18型（登录号NC_001357.1）、HPV68b型（登录号FR751039.1）及HPV45型（登录号X74479.1）的参考基因组。后续采用Hisat2 v2.1.0比对工具、Cufflinks v2.2.1、Cuffmerge及Cuffdiff对处理后的二进制比对映射（Binary Alignment/Map, BAM）文件进行进一步分析。包含病毒转录组序列的经过排序的BAM文件被标注为"排序BAM文件"。HPV16型转录组数据及其以FPKM（Fragments Per Kilobase of transcript per Million mapped reads, FPKM）表示的表达水平，可通过整合基因组浏览器（Integrative Genomics Viewer, IGV）软件进行可视化展示。映射至病毒参考序列后的总读段数与病毒读段数，收录于"高危HPV基因及剪接异构体FPKM追踪文件"中；剪接转录本被命名为CUFF。4种高危HPV（High-risk HPV, HR-HPV）型别的整合位点被分析并展示于"融合文件"中。通过IGV可视化分析，发现4种HPV型别的剪接接头均位于E6与E1区域内。针对E6区域，其5'端存在1个剪接供体（splicing donor, SD），3'端存在多种剪接受体（splicing acceptor, SA）位点，具体如下：在HPV16型阳性宫颈癌细胞系CaSki与SiHa中，共发现3处剪接接头：SD226^SA409（E6*I）、SD226^SA526（E6*II）及SD226^SA742（E6*X）；在HPV18型阳性细胞系HeLa中，发现2处剪接接头：SD233^SA416（E6*I）、SD233^SA635；在HPV45型阳性细胞系MS751中，剪接接头为SD230^SA412（E6*I）、SD230^SA640；在HPV68b型阳性细胞系ME180中，剪接接头为SD129^SA311（E6*I）、SD129^SA406。在CaSki与SiHa的E1区域内发现的剪接接头包括：SD880^SA3358、SD880^SA3361、SD880^SA3391、SD880^SA1726、SD880^SA2405、SD880^SA2582（E1C）、SD880^SA2709（E2*）、SD880^SA3020、SD880^SA3078、SD880^SA3329、SD577^SA6810、SD898^SA1725、SD1302^SA2709、SD1302^SA3358（E2C）、SD1760^SA3391、SD1263^SA3391、SD2309^SA3461；其余剪接形式包括：SD96^SA1063、SD226^SA2709（E6*IV）、SD226^SA3329、SD226^SA3358（E6*III）、SD226^SA3361、SD226^SA3391及SD579^SA6809。HPV18型HeLa细胞的E1区域剪接接头为：SD929^SA2779、SD977^SA1836、SD1342^SA1436、SD1987^SA2047；同时在其E7区域发现1处剪接事件：SD599^SA619。HPV68b型ME180细胞的E1区域剪接接头为：SD839^SA2586、SD683^SA2586、SD839^SA2586；而HPV45型MS751细胞中未检测到E1区域剪接接头。