run_metadata: 61689
This data as json
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| 61689 | SRR12951276 | SRX9404383 | SRS7622158 | SRP290217 | PRJNA673345 | Zebrafish as an animal model for the antiviral RNA interference pathway | GSE160475 | Transcriptome Analysis | We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus SINV vesicular stomatitis virus VSV and nodamura virus NoV. We find that SINV and NoV viruses induce the production of virus derived small interfering RNAs vsiRNAs the hallmark of antiviral RNAi with a preference of 22 nucleotides in length post infection of larval zebrafish. Meanwhile the suppressor of RNAi VSR protein NoV B2 may affect the accumulation of the NoV virus in zebrafish. Overall design: 5 virus derived small RNA from zebrafish infected with different viruses was detected by small RNA seq. | SINV: zebrafish 3 dpi | GSM4873784 | source name:zebrafish whole body|tissue:whole body|infection:SINV|injection way:microinjection|zebrafish background:AB | SINV: zebrafish 3 dpi | Sequenced reads were trimmed for adaptor sequence then mapped to virus genome using bowtie 1.1.2 with perfect match. Genome build: AF174533.1 AF174534.1;J02363.1;NC 001560.1 Supplementary files format and content: mapping results files generated by bowtie1.1.2 | zebrafish whole body | Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA. | tissue:whole body|infection:SINV|injection way:microinjection|zebrafish background:AB | GSM4873784 | GSM4873784: SINV: zebrafish 3 dpi; Danio rerio; ncRNA Seq | GSM4873784 | 1 | Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA. | GEO Accession:GSM4873784 | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP290217 | 4_LY215.fq.gz | fastq | 1328044600.0 | 26560892.0 | GSM4873784 r1 | 0:50 1:0 | A:383401484;C:303337306;G:339848340;T:301397824;N:59646 | 50 | 0 | 383401484 | 303337306 | 339848340 | 301397824 | 59646 | SRX9404383 | SRS7622158 | SRA1151114 | GEO | Fudan University | 1 | 0.83242 | 0.11559 | 0.93634 | 0.53516 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | size_fractionation | trueseq | bulk | unknown | unknown | China | 2020-10-30 | Undetermined | Larval | Trunk | Surface Structure |