RNAseq data of Aedes aegypti with variable extrinsic incubation periods for dengue virus

In this study, we compared the transcriptomes of Aedes aegypti mosquitoes of varying extrinsic incubation period (EIP) lengths with the goal of identifying genes whose expression patterns are associated with the EIP trait. To measure EIP, mosquitoes were orally fed with blood containing DENV-3 and their saliva sampled every two days to be assayed for the presence of virions. When virions are detected in the saliva of a mosquito, the whole body is collected the following day. These mosquitoes are designated DENGUE or D in the data. As a negative control, age-matched mosquitoes were fed non-viremic blood in parallel and collected at the appropriate timepoints to match EIP groups. These mosquitoes are designated BLOOD or B in the data. Six individual mosquitoes were sampled for each EIP group (6, 8, 10, and 12 days-post infection) for sequencing. To test for a significant relationship between DPI EIP and DENV infection that was not a response to blood-feeding, the following linear model was used: expression = sample + SV1 + SV2 + SV3 + SV4 + SV5 + SV6 + SV7 + SV8 + SV9 + SV10 + EIP + treatment + EIP x treatment where sample was a random effect, SV1-10 represents 10 surrogate variables fit independently as fixed, EIP was the categorical fixed effect of days-post-infection that DENV was detected in saliva, and treatment was a fixed effect with two levels (DENGUE or BLOOD). A significant interaction between EIP and treatment indicated that the differences in expression for each EIP group were not the same for DENGUE and BLOOD mosquitoes. All models were run using LIMMA in R.

本研究对不同外潜伏期（extrinsic incubation period, EIP）时长的埃及伊蚊（Aedes aegypti）开展转录组比较分析，旨在筛选出表达模式与EIP性状相关的基因。为测定EIP，研究人员将伊蚊经口喂食含登革病毒3型（DENV-3）的血液，并每隔两日采集其唾液以检测病毒粒子是否存在。当在伊蚊唾液中检测到病毒粒子后，于次日采集其整虫体，此类伊蚊在数据中被标记为DENGUE组（简称D组）。作为阴性对照（negative control），本研究同步设置年龄匹配的伊蚊喂食非病毒血症血液，并按照与EIP组匹配的时间点采集样本，此类伊蚊在数据中被标记为BLOOD组（简称B组）。针对每个EIP组（感染后6、8、10和12天），各采集6只伊蚊个体用于转录组测序。为探究不依赖于吸血行为的感染后天数（days-post infection, DPI）对应的EIP与DENV感染之间的显著关联，本研究采用如下线性模型：
表达量 = 样本 + SV1 + SV2 + SV3 + SV4 + SV5 + SV6 + SV7 + SV8 + SV9 + SV10 + EIP + 处理 + EIP×处理
其中，样本为随机效应（random effect）；SV1至SV10代表10个独立拟合的固定替代变量（surrogate variable）；EIP为分类固定效应，对应唾液中检测到DENV时的感染后天数；处理为包含两个水平（DENGUE组与BLOOD组）的固定效应。若EIP与处理间存在显著交互作用，则表明各EIP组的基因表达差异在DENGUE组与BLOOD组伊蚊中并不一致。所有模型均通过R语言中的LIMMA包运行。