run_metadata: 32030
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 32030 | SRR28960829 | SRX24490432 | SRS21239708 | SRP506336 | PRJNA1108487 | First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response | PRJNA1108487 | Other | Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted. | Empty RGNNV 3 | strain:wild type|isolate:11|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal | Rna Seq of zebrafish larvae | Empty RGNNV 3 | Empty RGNNV 3 | RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP506336 | C-V3_1.fastq.gz C-V3_2.fastq.gz | fastq fastq | 4990782540.0 | 16525770.0 | C V3 1.fastq.gz | 0:151 1:151 | A:1370883963;C:1121960304;G:1139361266;T:1358553278;N:23729 | 151 | 151 | 1370883963 | 1121960304 | 1139361266 | 1358553278 | 23729 | SRX24490432 | SRS21239708 | SRA1861741 | IIM-CSIC|Immunology and Genomics | IIM-CSIC | 2 | 0.94311 | 0.94426 | 0.10644 | 0.10476 | 0.65535 | 0.65756 | 0.46134 | 0.44955 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | random_priming | unknown | bulk | unknown | unknown | Spain | 2024-05-08 | Larval | Larval | Whole Organism | All anatomical structures |