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| Status |
Public on Feb 25, 2019 |
| Title |
C6/36_Melpop rep3 |
| Sample type |
SRA |
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| Source name |
Cell culture
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| Organism |
Aedes albopictus |
| Characteristics |
clone: C6/36
treatment: with wMelpop symbiont
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| Treatment protocol |
The C6/36 cells, in which the endosymbiont wMelPop, stably replicates (referred here as wMelPop-C6/36 cells) were grown in the same medium and conditions as mentioned above.
Naïve C6/36 and wMelPop-C6/36 cells were infected with DENV2 in triplicate T-75 flasks. DENV2 stock was diluted in 2% FBS-supplemented with maintenance medium and added to 70% confluent monolayer cells at MOI of 1. Cells were incubated for an hour at room temperature. Then, the culture media were replaced with maintenance medium containing 5% FBS and the cells were incubated in a humidified 5% CO2 chamber at 37 oC.
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| Growth protocol |
The C6/36 cells were grown in minimum essential medium (MEM) containing 5% FBS, 2mM L-glutamine, 25 147 mM HEPES, pH 7.2, 1 mM sodium pyruvate, 1x non-essential amino acids, 100 U/ml 148 penicillin and 100 μg/ml streptomycin at 28 oC.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs from monolayer of C6/36 cells were extracted with Trizol (Ambion Life Technologies) according to the manufacturer’s instructions. RNA quantity and integrity were determined on an Agilent 2100 Bioanalyzer. After three to five days post infection, culture supernatants were collected after centrifugation at 3,000 rpm for 5 minutes. Monolayer cells were used for RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
C6/36 cells with wMelpop symbiont
c636_mpop_3_vs_albo_w_annot_gene_count.txt
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| Data processing |
Raw reads were first screened using ssaha2 (Ning, Cox and Mullikin, 2001) and the UniVec database (accessed July 7th, 2013) to remove vector sequences, adapters, linkers, and primers commonly used in cloning cDNA or genomic DNA as well as Ae. albopictus rRNA sequences (GenBank accession L22060.1). After ssaha2 screening, cleaned reads were further filtered using SolexaQA V2.2 to retain contiguous reads longer than 50 bp with phred quality scores higher than 30.
Cleaned reads were mapped to the annotated scaffolds in the Ae. albopictus genome (Chen et al. 2015), using Hisat2 (Version 2.0.4).
Contigs were assembled from the sorted BAM files using Stringtie (Version 1.3.0). Transcripts were constructed and merged from all 11 libraries. Transcript counts at the gene level, not the isoform level, were obtained using Ballgown (Version 2.7). Reads counts were then processed in edgeR (Chen et al. 2015) in the R software environment (www.r-project.org).
Differentially expressed (DE) genes were identified as having an absolute value of log2 fold-change greater than 1 with a Benjamini-Hochberg (FDR)-corrected p-value less than 0.05.
Genome_build: AaloF1
Supplementary_files_format_and_content: tab-delimited text files include raw gene read numbers for each Sample ...
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| Submission date |
Jan 24, 2019 |
| Last update date |
Feb 25, 2019 |
| Contact name |
Klaudia Kuranda |
| Organization name |
Spark Therapeutics
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| Department |
Data Sciences
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| Street address |
3737 Market St
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL26091 |
| Series (1) |
| GSE125580 |
wMelpop strain of Wolbachia infection of Aedes albopictus mosquito C6/36 cells modulates dengue virus-induced host cellular transcripts and induces critical sequence alterations in dengue viral genome |
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| Relations |
| BioSample |
SAMN10805337 |
| SRA |
SRX5287013 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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