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Data released on December 31, 2017

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

Miller, J, R; Koren, S; Dilley, K, A; Puri, V; Brown, D, M; Harkins, D, M; Thibaud-Nissen, F; Rosen, B; Chen, X; Tu, Z; Sharakhov, I, V; Sharakhova, M, V; Sebra, R; Stockwell, T, B; Bergman, N, H; Sutton, G, G; Phillippy, A, M; Piermarini, P, M; Shabman, R, S (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 RIS BibTeX Text

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.

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Accessions (data included in GigaDB):

GenBank: MNAF02000000
GenBank: GCA_001876365.2

Keywords:

aedes albopictus c6/36 cell line genome assembly mosquito 

Genomic

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Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
DHSSDB_A_albo_C6367160forest day mosquitoAsian tiger mosquitoAedes albopictus Description:DNA extracted from Aedes albopictus C...
Molecular data type:DNA
Alternative accession-BioSample:SAMN05908721
...
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ZIKVRS_ZIKVDHS_00001 7160forest day mosquitoAsian tiger mosquitoAedes albopictus Description:RNA extracted from Aedes albopictus C6...
Molecular data type:RNA
Alternative accession-BioSample:SAMN06691554
...
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ZIKVRS_ZIKVDHS_00002 7160forest day mosquitoAsian tiger mosquitoAedes albopictus Description:RNA extracted from Aedes albopictus C6...
Molecular data type:RNA
Alternative accession-BioSample:SAMN06691555
...
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ZIKVRS_ZIKVDHS_00003 7160forest day mosquitoAsian tiger mosquitoAedes albopictus Description:RNA extracted from Aedes albopictus C6...
Molecular data type:RNA
Alternative accession-BioSample:SAMN06691556
...
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ZIKVRS_ZIKVDHS_00004 7160forest day mosquitoAsian tiger mosquitoAedes albopictus Description:RNA extracted from Aedes albopictus C6...
Molecular data type:RNA
Alternative accession-BioSample:SAMN06691557
...
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ZIKVRS_ZIKVDHS_00005 7160forest day mosquitoAsian tiger mosquitoAedes albopictus Description:RNA extracted from Aedes albopictus C6...
Molecular data type:RNA
Alternative accession-BioSample:SAMN06691558
...
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ZIKVRS_ZIKVDHS_00006 7160forest day mosquitoAsian tiger mosquitoAedes albopictus Description:RNA extracted from Aedes albopictus C6...
Molecular data type:RNA
Alternative accession-BioSample:SAMN06691559
...
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ZIKVRS_ZIKVDHS_00007 7160forest day mosquitoAsian tiger mosquitoAedes albopictus Description:RNA extracted from Aedes albopictus C6...
Molecular data type:RNA
Alternative accession-BioSample:SAMN06691560
...
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ZIKVRS_ZIKVDHS_00008 7160forest day mosquitoAsian tiger mosquitoAedes albopictus Description:RNA extracted from Aedes albopictus C6...
Molecular data type:RNA
Alternative accession-BioSample:SAMN06691561
...
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ZIKVRS_ZIKVDHS_00009 7160forest day mosquitoAsian tiger mosquitoAedes albopictus Description:RNA extracted from Aedes albopictus C6...
Molecular data type:RNA
Alternative accession-BioSample:SAMN06691562
...
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Displaying 1-10 of 31 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
annotationUNKNOWN65.17 MB2017-12-28
annotationGFF9.11 MB2017-12-28
annotationUNKNOWN1.03 KB2017-12-28
annotationUNKNOWN16.88 MB2017-12-28
Genome sequenceFASTA674.56 MB2017-12-28
imageTIF903.7 KB2017-12-28
imageTIF1.41 MB2017-12-28
imageTIF1.61 MB2017-12-28
imageTIF1.17 MB2017-12-28
imageTIF1.13 MB2017-12-28
Displaying 1-10 of 16 File(s).

History:

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