run_metadata: 51861
This data as json
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| 51861 | SRR8888287 | SRX5674005 | SRS4616284 | SRP192333 | PRJNA532380 | Danio rerio SVCV infection | PRJNA532380 | Other | Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response. | WTC2 | WTC2 | strain:WT|isolate:2|age:6 mpf|dev stage:adult|sex:pooled male and female|tissue:kidney|biomaterial provider:IIM|birth date:2016|birth location:IIM|collected by:Patry Pereiro and Marga Alvarez|collection date:2016|death date:2016|health state:control|isolation source:WTC2|BioSampleModel:Model organism or animal | WTC2 | WTC2 | WTC2 | eukaryotic mRNA was extracted from total RNA using oligo dT magnetic beads and cleaved into short fragments using fragmentation buffer. A cDNA library compatible with the Illumina NGS technology was then prepared from the fragmented mRNA via reverse transcription second strand synthesis and ligation of specific adapters paired ends post cDNA purification using the QIAquick PCR Purification Kit Qiagen. The amount of cDNA in each library was quantified through spectrofluorometric analysis using the Qbit system. Next generation sequencing was performed using Illumina HiSeq 4000 technology | RNA-Seq | TRANSCRIPTOMIC | unspecified | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP192333 | WTC2_2.fastq.gz WTC2_1.fastq.gz | fastq fastq | 9232541906.0 | 45705653.0 | WTC2 1.fastq.gz | 0:101 1:101 | A:2377508195;C:2235019239;G:2220061555;T:2399805579;N:147338 | 101 | 101 | 2377508195 | 2235019239 | 2220061555 | 2399805579 | 147338 | SRX5674005 | SRS4616284 | SRA873264 | IIM - CSIC|Biotechnology and Aquaculture | IIM - CSIC | 2 | 0.93618 | 0.93685 | 0.0348 | 0.03356 | 0.69891 | 0.7026 | 0.48034 | 0.47779 | 101 | 101 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | unknown | unknown | bulk | unknown | unknown | Spain | 2019-04-12 | Adult | Adult | Kidney | Renal System |