run_metadata: 9848
This data as json
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| 9848 | ERR4029253 | ERX4030569 | ERS4514122 | ERP121190 | PRJEB37851 | Zebrafish il 4 il 10 regulated immunity in gills | E-MTAB-8958 | Transcriptome Analysis | The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. | ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 | Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. | Sample 14 | SAMEA6786443 | UNIVERSITY OF MANCHESTER | ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786443|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 14|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 14|scientific name:Danio rerio | Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills | E MTAB 8958:Sample 14 p | Sample 14 p | Zebrafish il 4 il 10 regulated immunity in gills | This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. | Experimental Factor: genotype:il4/13b / | RNA-Seq | TRANSCRIPTOMIC | RANDOM | PAIRED | ILLUMINA | Illumina HiSeq 4000 | ERP121190 | Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills | ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 | FB2_S18_R1_001.fastq.gz FB2_S18_R2_001.fastq.gz | fastq fastq | 5789923311.0 | 38517674.0 | E MTAB 8958:FB2 S18 R | 0:75.18 1:75.14 | A:1520250885;C:1354960735;G:1336204150;T:1565011084;N:13496457 | 75 | 75 | 1520250885 | 1354960735 | 1336204150 | 1565011084 | 13496457 | ERX4030569 | ERS4514122 | ERA2508092 | UNIVERSITY OF MANCHESTER|European Nucleotide Archive | UNIVERSITY OF MANCHESTER|European Nucleotide Archive | 2 | 0.91863 | 0.91917 | 0.08923 | 0.08753 | 0.68848 | 0.68883 | 0.5042 | 0.50799 | 76 | 76 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | random_priming | trueseq | bulk | unknown | unknown | United Kingdom | 2020-04-16 | Adult | Adult | Gill | Respiratory System |