Supporting data for "Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation"

Dataset type: Genomic
Data released on December 31, 2017

Miller JR; Koren S; Dilley KA; Puri V; Brown DM; Harkins DM; Thibaud-Nissen F; Rosen B; Chen X; Tu Z; Sharakhov IV; Sharakhova MV; Sebra R; Stockwell TB; Bergman NH; Sutton GG; Phillippy AM; Piermarini PM; Shabman RS (2017): Supporting data for "Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation" GigaScience Database. http://dx.doi.org/10.5524/100401

DOI10.5524/100401

The 50-year old Aedes albopictus C6/36 cell line is a resource for the detection, amplification, and analysis of mosquito-borne viruses including Zika, dengue, and chikungunya. The cell line is derived from an unknown number of larvae from an unspecified strain of Aedes albopictus mosquitoes. Toward improved utility of the cell line for research in virus transmission, we present an annotated assembly of the C6/36 genome.
The C6/36 genome assembly has the largest contig N50 (3.3 Mbp) of any mosquito assembly, presents the sequences of both haplotypes for most of the diploid genome, reveals independent null mutations in both alleles of the Dicer locus, and indicates a male-specific genome. Gene annotation was computed with publicly available mosquito transcript sequences. Gene expression data from cell line RNA sequence identified enrichment of growth-related pathways and conspicuous deficiency in aquaporins and inward rectifier K+ channels. As a test of utility, RNA sequence data from Zika-infected cells was mapped to the C6/36 genome and transcriptome assemblies. Host subtraction reduced the data set by 89%, enabling faster characterization of non-host reads.
The C6/36 genome sequence and annotation should enable additional uses of the cell line to study arbovirus vector interactions and interventions aimed at restricting the spread of human disease.

Additional details

Read the peer-reviewed publication(s):

Miller, J. R., Koren, S., Dilley, K. A., Puri, V., Brown, D. M., Harkins, D. M., … Shabman, R. S. (2018). Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation. GigaScience, 7(3). doi:10.1093/gigascience/gix135

Accessions (data included in GigaDB):

GenBank: MNAF02000000
GenBank: GCA_001876365.2





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
ZIKVRS_ZIKVDHS_00020 7160forest day mosquitoAsian tiger mosquitoAedes albopictus Description:RNA extracted from Aedes albopictus C6...
Molecular data type:RNA
Alternative accession-BioSample:SAMN06691573
...
+
ZIKVRS_ZIKVDHS_00021 7160forest day mosquitoAsian tiger mosquitoAedes albopictus Description:RNA extracted from Aedes albopictus C6...
Molecular data type:RNA
Alternative accession-BioSample:SAMN06691574
...
+
ZIKVRS_ZIKVDHS_00022 7160forest day mosquitoAsian tiger mosquitoAedes albopictus Description:RNA extracted from Aedes albopictus C6...
Molecular data type:RNA
Alternative accession-BioSample:SAMN06691575
...
+
ZIKVRS_ZIKVDHS_00023 7160forest day mosquitoAsian tiger mosquitoAedes albopictus Description:RNA extracted from Aedes albopictus C6...
Molecular data type:RNA
Alternative accession-BioSample:SAMN06691576
...
+
ZIKVRS_ZIKVDHS_00024 7160forest day mosquitoAsian tiger mosquitoAedes albopictus Description:RNA extracted from Aedes albopictus C6...
Molecular data type:RNA
Alternative accession-BioSample:SAMN06691577
...
+
ZIKVRS_ZIKVDHS_00025 7160forest day mosquitoAsian tiger mosquitoAedes albopictus Description:RNA extracted from Aedes albopictus C6...
Molecular data type:RNA
Alternative accession-BioSample:SAMN06691578
...
+
ZIKVRS_ZIKVDHS_00026 7160forest day mosquitoAsian tiger mosquitoAedes albopictus Description:RNA extracted from Aedes albopictus C6...
Molecular data type:RNA
Alternative accession-BioSample:SAMN06691579
...
+
ZIKVRS_ZIKVDHS_00027 7160forest day mosquitoAsian tiger mosquitoAedes albopictus Description:RNA extracted from Aedes albopictus C6...
Molecular data type:RNA
Alternative accession-BioSample:SAMN06691580
...
+
ZIKVRS_ZIKVDHS_00028 7160forest day mosquitoAsian tiger mosquitoAedes albopictus Description:RNA extracted from Aedes albopictus C6...
Molecular data type:RNA
Alternative accession-BioSample:SAMN06691581
...
+
ZIKVRS_ZIKVDHS_00029 7160forest day mosquitoAsian tiger mosquitoAedes albopictus Description:RNA extracted from Aedes albopictus C6...
Molecular data type:RNA
Alternative accession-BioSample:SAMN06691582
...
+
Displaying 21-30 of 31 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
OtherPDF2.43 MB2017-12-28
imageTIF1.41 MB2017-12-28
imageTIF903.7 KB2017-12-28
imageTIF1.17 MB2017-12-28
Genome sequenceFASTA674.56 MB2017-12-28
annotationUNKNOWN1.03 KB2017-12-28
ImageTIF1.34 MB2017-12-28
imageTIF1.61 MB2017-12-28
imageTIF1.13 MB2017-12-28
protein sequenceFASTA10.33 MB2017-12-28
Displaying 1-10 of 16 File(s).
Date Action
January 1, 2018 Dataset publish
March 30, 2018 Manuscript Link added : 10.1093/gigascience/gix135