Dataset

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

Monash University
Cassandra Koh (Aggregated by) Elizabeth McGraw (Aggregated by) Nick Appleton (Aggregated by) Scott Allen (Aggregated by)
Viewed: [[ro.stat.viewed]] Cited: [[ro.stat.cited]] Accessed: [[ro.stat.accessed]]
ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=info:doi10.26180/5bb0d5ae69035&rft.title=RNAseq data of Aedes aegypti with variable extrinsic incubation periods for dengue virus&rft.identifier=http://doi.org/10.26180/5bb0d5ae69035&rft.publisher=Monash University&rft.description=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.&rft.creator=Nick Appleton&rft.creator=Scott Allen&rft.creator=Elizabeth McGraw&rft.creator=Cassandra Koh&rft.date=2018&rft_rights=&rft_subject=Aedes Aegypti&rft_subject=Dengue&rft_subject=Extrinsic Incubation Period&rft.type=dataset&rft.language=English Access the data

Licence & Rights:

Other view details
Cc-by 4.0

Full description

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.

Issued: 2018-10-21

Click to explore relationships graph
Subjects

User Contributed Tags    

Login to tag this record with meaningful keywords to make it easier to discover