Fossil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA282142 | ENA |
REPOSITORIES: ENA
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Project description:We attempted to characterize the transcriptome of the chicken embryo during Newcastle disease virus (NDV) infection using RNA-sequencing analysis. The cDNAs derived from Total RNA of the pooled visceral tissues infected with F48E9 or La Sota were sequenced and analysed. The collected clean reads covered about 4.02% (2,341,868 reads) of the entire F48E8 reference sequence, while only 0.02% reads (13,886) were mapped to the La Sota genome. RNA-Seq datasets from groups La Sota, F48E9 and control, were respectively mapped to 71.76%, 68.55% and 70.05% of the reference genome Galgal 4.73. Compared with the control, 2,035 and 1,604 differentially expressed genes of hosts were found responding to F48E9 and La Sota infection, respectively. GO and KEGG pathway enriched various signalling pathways with elements playing roles in enhancing or preventing viral infection, like IFP35, NMI, Mx, OAS*A, IFITM5, STAT1 and IFNβ. So far, we know that velogenic NDV made far more transcripts during infection and caused significant impact on the host, showing a large number of genes in various pathways at high levels of expression.
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Project description:Usually, unmapped reads have been considered as useless and been trashed or ignored. Here, we develop a strategy to mining the full length sequence by unmapped reads combining with specific reverse transcription primers design and high throughput sequencing. In this study, we salvage 36 unmapped reads from standard RNA-Seq data(GSM3188619) and randomly select one 149 bp read as a model(CTGGTGCCATAATTCAGGGAACTGTGTTCTTGATGTACTATCTGAGACATTTGTGCTTCCCCCCATCCAGCTATCAGGCTGTTAGGCAATGCACTTCTAGGAATTAGAATTCTATAAGGAATCTCATGCTGGAAGAACAAAAAGACCCA ). Specific reverse transcription primers(5' end:CTGGTGCCATAATTCAGGGA, 3' end:GGATCTTCACGTAACGGATTGT) are designed to amplify its both ends, followed by next generation sequencing. Then we use a statistical model base on power law distribution to estimate its integrality and significance. Further, we validate it by Sanger sequencing. The result shows that the full length is 1,556 bp, with InDel mutation in microsatellite structure. This would be a useful strategy to extract the sequences information from the unmapped RNA-seq data.
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