metadata: run_metadata: 20 rows where experiment.library_selection = "RANDOM", experiment.platform = "ILLUMINA" and tissue_curation

20 rows where experiment.library_selection = "RANDOM", experiment.platform = "ILLUMINA" and tissue_curation_coarse = "Respiratory System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
9842	9842	ERR4029259	ERX4030575	ERS4514128	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 4	SAMEA6786449	UNIVERSITY OF MANCHESTER	ENA FIRST PUBLIC:2020 05 28T17:07:47Z\|ENA LAST UPDATE:2020 04 16T14:58:15Z\|External Id:SAMEA6786449\|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 4\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|organism part:gill\|sample name:E MTAB 8958:Sample 4\|scientific name:Danio rerio	Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills	E MTAB 8958:Sample 4 p	Sample 4 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:wild type genotype	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	FB4_S41_R1_001.fastq.gz FB4_S41_R2_001.fastq.gz	fastq fastq	4354809436.0	29071030.0	E MTAB 8958:FB4 S41 R	0:74.90 1:74.90	A:1140431810;C:1005396495;G:1008528915;T:1171220102;N:29232114	74	74	1140431810	1005396495	1008528915	1171220102	29232114	ERX4030575	ERS4514128	ERA2508092	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	2	0.91143	0.91076	0.10123	0.09941	0.68235	0.68452	0.48713	0.48998	76	74	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
9843	9843	ERR4029258	ERX4030574	ERS4514127	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 3	SAMEA6786448	UNIVERSITY OF MANCHESTER	ENA FIRST PUBLIC:2020 05 28T17:07:47Z\|ENA LAST UPDATE:2020 04 16T14:58:15Z\|External Id:SAMEA6786448\|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 3\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|organism part:gill\|sample name:E MTAB 8958:Sample 3\|scientific name:Danio rerio	Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills	E MTAB 8958:Sample 3 p	Sample 3 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:wild type genotype	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	FB3_S40_R1_001.fastq.gz FB3_S40_R2_001.fastq.gz	fastq fastq	3973860397.0	26559713.0	E MTAB 8958:FB3 S40 R	0:74.80 1:74.82	A:1038749031;C:917944667;G:920080717;T:1066160216;N:30925766	74	74	1038749031	917944667	920080717	1066160216	30925766	ERX4030574	ERS4514127	ERA2508092	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	2	0.91065	0.90981	0.10133	0.09911	0.68789	0.68945	0.47182	0.49996	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
9844	9844	ERR4029257	ERX4030573	ERS4514126	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 2	SAMEA6786447	UNIVERSITY OF MANCHESTER	ENA FIRST PUBLIC:2020 05 28T17:07:47Z\|ENA LAST UPDATE:2020 04 16T14:58:15Z\|External Id:SAMEA6786447\|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 2\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|organism part:gill\|sample name:E MTAB 8958:Sample 2\|scientific name:Danio rerio	Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills	E MTAB 8958:Sample 2 p	Sample 2 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:wild type genotype	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_S39_R1_001.fastq.gz FB2_S39_R2_001.fastq.gz	fastq fastq	4135184845.0	27517010.0	E MTAB 8958:FB2 S39 R	0:75.15 1:75.13	A:1084253902;C:962303819;G:961163738;T:1111949967;N:15513419	75	75	1084253902	962303819	961163738	1111949967	15513419	ERX4030573	ERS4514126	ERA2508092	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	2	0.91098	0.91057	0.09468	0.09311	0.68095	0.68282	0.49982	0.50146	75	75	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
9845	9845	ERR4029256	ERX4030572	ERS4514125	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 1	SAMEA6786446	UNIVERSITY OF MANCHESTER	ENA FIRST PUBLIC:2020 05 28T17:07:47Z\|ENA LAST UPDATE:2020 04 16T14:58:15Z\|External Id:SAMEA6786446\|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 1\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|organism part:gill\|sample name:E MTAB 8958:Sample 1\|scientific name:Danio rerio	Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills	E MTAB 8958:Sample 1 p	Sample 1 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:wild type genotype	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 06 17	FB1_S38_R1_001.fastq FB1_S38_R2_001.fastq	fastq fastq	4651073045.0	31021879.0	E MTAB 8958:FB1 S38 R	0:74.96 1:74.97	A:1225305023;C:1072643957;G:1069905162;T:1255950159;N:27268744	74	74	1225305023	1072643957	1069905162	1255950159	27268744	ERX4030572	ERS4514125	ERA2508092	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	2	0.91441	0.91282	0.10095	0.09913	0.686	0.68745	0.49433	0.5047	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
9846	9846	ERR4029255	ERX4030571	ERS4514124	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 16	SAMEA6786445	UNIVERSITY OF MANCHESTER	ENA FIRST PUBLIC:2020 05 28T17:07:47Z\|ENA LAST UPDATE:2020 04 16T14:58:15Z\|External Id:SAMEA6786445\|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 16\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:il4/13b / \|organism part:gill\|sample name:E MTAB 8958:Sample 16\|scientific name:Danio rerio	Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills	E MTAB 8958:Sample 16 p	Sample 16 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	FB4_S20_R1_001.fastq.gz FB4_S20_R2_001.fastq.gz	fastq fastq	5961540086.0	39717871.0	E MTAB 8958:FB4 S20 R	0:75.07 1:75.03	A:1565483441;C:1390303898;G:1372759826;T:1611361282;N:21631639	75	75	1565483441	1390303898	1372759826	1611361282	21631639	ERX4030571	ERS4514124	ERA2508092	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	2	0.90959	0.90989	0.0925	0.09172	0.68787	0.68929	0.49093	0.49057	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
9847	9847	ERR4029254	ERX4030570	ERS4514123	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 15	SAMEA6786444	UNIVERSITY OF MANCHESTER	ENA FIRST PUBLIC:2020 05 28T17:07:47Z\|ENA LAST UPDATE:2020 04 16T14:58:15Z\|External Id:SAMEA6786444\|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 15\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:il4/13b / \|organism part:gill\|sample name:E MTAB 8958:Sample 15\|scientific name:Danio rerio	Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills	E MTAB 8958:Sample 15 p	Sample 15 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	FB3_S19_R1_001.fastq.gz FB3_S19_R2_001.fastq.gz	fastq fastq	6835575760.0	45515064.0	E MTAB 8958:FB3 S19 R	0:75.11 1:75.07	A:1802176562;C:1589590146;G:1564279107;T:1858606235;N:20923710	75	75	1802176562	1589590146	1564279107	1858606235	20923710	ERX4030570	ERS4514123	ERA2508092	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	2	0.90945	0.91123	0.09519	0.09378	0.67963	0.67961	0.49246	0.49476	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
9848	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
9849	9849	ERR4029252	ERX4030568	ERS4514121	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 13	SAMEA6786442	UNIVERSITY OF MANCHESTER	ENA FIRST PUBLIC:2020 05 28T17:07:47Z\|ENA LAST UPDATE:2020 04 16T14:58:15Z\|External Id:SAMEA6786442\|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 13\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:il4/13b / \|organism part:gill\|sample name:E MTAB 8958:Sample 13\|scientific name:Danio rerio	Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills	E MTAB 8958:Sample 13 p	Sample 13 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	FB1_S17_R1_001.fastq.gz FB1_S17_R2_001.fastq.gz	fastq fastq	6951804793.0	46295025.0	E MTAB 8958:FB1 S17 R	0:75.10 1:75.06	A:1827618209;C:1618955946;G:1595802123;T:1884739421;N:24689094	75	75	1827618209	1618955946	1595802123	1884739421	24689094	ERX4030568	ERS4514121	ERA2508092	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	2	0.90991	0.90972	0.09297	0.09193	0.68284	0.68392	0.49878	0.5017	74	75	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
9850	9850	ERR4029251	ERX4030567	ERS4514120	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 20	SAMEA6786441	UNIVERSITY OF MANCHESTER	ENA FIRST PUBLIC:2020 05 28T17:07:47Z\|ENA LAST UPDATE:2020 04 16T14:58:15Z\|External Id:SAMEA6786441\|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 20\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:il4/13a / ; il4/13b / \|organism part:gill\|sample name:E MTAB 8958:Sample 20\|scientific name:Danio rerio	Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills	E MTAB 8958:Sample 20 p	Sample 20 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:il4/13a / ; 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	FB4_S44_R1_001.fastq.gz FB4_S44_R2_001.fastq.gz	fastq fastq	9629684100.0	64667395.0	E MTAB 8958:FB4 S44 R	0:74.47 1:74.44	A:2552333346;C:2176006333;G:2180111416;T:2614191329;N:107041676	74	74	2552333346	2176006333	2180111416	2614191329	107041676	ERX4030567	ERS4514120	ERA2508092	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	2	0.90795	0.90756	0.10044	0.09789	0.6888	0.69256	0.50043	0.4932	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
9851	9851	ERR4029250	ERX4030566	ERS4514119	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 19	SAMEA6786440	UNIVERSITY OF MANCHESTER	ENA FIRST PUBLIC:2020 05 28T17:07:47Z\|ENA LAST UPDATE:2020 04 16T14:58:15Z\|External Id:SAMEA6786440\|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 19\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:il4/13a / ; il4/13b / \|organism part:gill\|sample name:E MTAB 8958:Sample 19\|scientific name:Danio rerio	Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills	E MTAB 8958:Sample 19 p	Sample 19 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:il4/13a / ; 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	FB3_S43_R1_001.fastq.gz FB3_S43_R2_001.fastq.gz	fastq fastq	11268744444.0	75088756.0	E MTAB 8958:FB3 S43 R	0:75.06 1:75.01	A:2983863814;C:2608268633;G:2555098938;T:3072413168;N:49099891	75	75	2983863814	2608268633	2555098938	3072413168	49099891	ERX4030566	ERS4514119	ERA2508092	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	2	0.9107	0.91089	0.09522	0.09428	0.69187	0.69266	0.49302	0.49463	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
9852	9852	ERR4029249	ERX4030565	ERS4514118	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 18	SAMEA6786439	UNIVERSITY OF MANCHESTER	ENA FIRST PUBLIC:2020 05 28T17:07:47Z\|ENA LAST UPDATE:2020 04 16T14:58:14Z\|External Id:SAMEA6786439\|INSDC center name:UNIVERSITY OF MANCHESTER\|INSDC first public:2020 05 28T17:07:47Z\|INSDC last update:2020 04 16T14:58:14Z\|INSDC status:public\|Submitter Id:E MTAB 8958:Sample 18\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:il4/13a / ; il4/13b / \|organism part:gill\|sample name:E MTAB 8958:Sample 18\|scientific name:Danio rerio	Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills	E MTAB 8958:Sample 18 p	Sample 18 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:il4/13a / ; 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_S42_R1_001.fastq.gz FB2_S42_R2_001.fastq.gz	fastq fastq	10434072067.0	69530304.0	E MTAB 8958:FB2 S42 R	0:75.06 1:75.01	A:2749500618;C:2426208950;G:2375421255;T:2834879202;N:48062042	75	75	2749500618	2426208950	2375421255	2834879202	48062042	ERX4030565	ERS4514118	ERA2508092	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	2	0.9084	0.90779	0.0926	0.0917	0.68809	0.68864	0.49817	0.49902	76	75	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
9853	9853	ERR4029248	ERX4030564	ERS4514117	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 17	SAMEA6786438	UNIVERSITY OF MANCHESTER	ENA FIRST PUBLIC:2020 05 28T17:07:47Z\|ENA LAST UPDATE:2020 04 16T14:58:14Z\|External Id:SAMEA6786438\|INSDC center name:UNIVERSITY OF MANCHESTER\|INSDC first public:2020 05 28T17:07:47Z\|INSDC last update:2020 04 16T14:58:14Z\|INSDC status:public\|Submitter Id:E MTAB 8958:Sample 17\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:il4/13a / ; il4/13b / \|organism part:gill\|sample name:E MTAB 8958:Sample 17\|scientific name:Danio rerio	Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills	E MTAB 8958:Sample 17 p	Sample 17 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:il4/13a / ; 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	FB1_S41_R1_001.fastq.gz FB1_S41_R2_001.fastq.gz	fastq fastq	12125040750.0	80781224.0	E MTAB 8958:FB1 S41 R	0:75.08 1:75.02	A:3129480022;C:2890038396;G:2819859086;T:3233228646;N:52434600	75	75	3129480022	2890038396	2819859086	3233228646	52434600	ERX4030564	ERS4514117	ERA2508092	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	2	0.91384	0.91301	0.10967	0.10615	0.69006	0.69041	0.51643	0.51985	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
9854	9854	ERR4029247	ERX4030563	ERS4514116	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 8	SAMEA6786437	UNIVERSITY OF MANCHESTER	ENA FIRST PUBLIC:2020 05 28T17:07:47Z\|ENA LAST UPDATE:2020 04 16T14:58:14Z\|External Id:SAMEA6786437\|INSDC center name:UNIVERSITY OF MANCHESTER\|INSDC first public:2020 05 28T17:07:47Z\|INSDC last update:2020 04 16T14:58:14Z\|INSDC status:public\|Submitter Id:E MTAB 8958:Sample 8\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:il4/13a / \|organism part:gill\|sample name:E MTAB 8958:Sample 8\|scientific name:Danio rerio	Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills	E MTAB 8958:Sample 8 p	Sample 8 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:il4/13a /	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	FB12_S49_R1_001.fastq.gz FB12_S49_R2_001.fastq.gz	fastq fastq	4223131851.0	28165494.0	E MTAB 8958:FB12 S49 R	0:74.95 1:74.99	A:1121514270;C:962554300;G:967294488;T:1146544647;N:25224146	74	74	1121514270	962554300	967294488	1146544647	25224146	ERX4030563	ERS4514116	ERA2508092	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	2	0.91639	0.91413	0.10604	0.10326	0.68162	0.68458	0.49921	0.50172	76	75	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
9855	9855	ERR4029246	ERX4030562	ERS4514115	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 7	SAMEA6786436	UNIVERSITY OF MANCHESTER	ENA FIRST PUBLIC:2020 05 28T17:07:47Z\|ENA LAST UPDATE:2020 04 16T14:58:14Z\|External Id:SAMEA6786436\|INSDC center name:UNIVERSITY OF MANCHESTER\|INSDC first public:2020 05 28T17:07:47Z\|INSDC last update:2020 04 16T14:58:14Z\|INSDC status:public\|Submitter Id:E MTAB 8958:Sample 7\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:il4/13a / \|organism part:gill\|sample name:E MTAB 8958:Sample 7\|scientific name:Danio rerio	Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills	E MTAB 8958:Sample 7 p	Sample 7 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:il4/13a /	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	FB11_S48_R1_001.fastq.gz FB11_S48_R2_001.fastq.gz	fastq fastq	4670407305.0	31054128.0	E MTAB 8958:FB11 S48 R	0:75.20 1:75.19	A:1234494738;C:1078360233;G:1084251975;T:1258088405;N:15211954	75	75	1234494738	1078360233	1084251975	1258088405	15211954	ERX4030562	ERS4514115	ERA2508092	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	2	0.92228	0.92038	0.09418	0.09222	0.68674	0.68862	0.48948	0.48842	75	75	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
9856	9856	ERR4029245	ERX4030561	ERS4514114	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 6	SAMEA6786435	UNIVERSITY OF MANCHESTER	ENA FIRST PUBLIC:2020 05 28T17:07:47Z\|ENA LAST UPDATE:2020 04 16T14:58:14Z\|External Id:SAMEA6786435\|INSDC center name:UNIVERSITY OF MANCHESTER\|INSDC first public:2020 05 28T17:07:47Z\|INSDC last update:2020 04 16T14:58:14Z\|INSDC status:public\|Submitter Id:E MTAB 8958:Sample 6\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:il4/13a / \|organism part:gill\|sample name:E MTAB 8958:Sample 6\|scientific name:Danio rerio	Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills	E MTAB 8958:Sample 6 p	Sample 6 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:il4/13a /	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	FB10_S47_R1_001.fastq.gz FB10_S47_R2_001.fastq.gz	fastq fastq	3970723047.0	26597167.0	E MTAB 8958:FB10 S47 R	0:74.63 1:74.66	A:1037861230;C:915437247;G:922979694;T:1056625196;N:37819680	74	74	1037861230	915437247	922979694	1056625196	37819680	ERX4030561	ERS4514114	ERA2508092	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	2	0.92474	0.92246	0.0934	0.0916	0.69106	0.69384	0.49058	0.48154	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
9857	9857	ERR4029244	ERX4030560	ERS4514113	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 5	SAMEA6786434	UNIVERSITY OF MANCHESTER	ENA FIRST PUBLIC:2020 05 28T17:07:47Z\|ENA LAST UPDATE:2020 04 16T14:58:14Z\|External Id:SAMEA6786434\|INSDC center name:UNIVERSITY OF MANCHESTER\|INSDC first public:2020 05 28T17:07:47Z\|INSDC last update:2020 04 16T14:58:14Z\|INSDC status:public\|Submitter Id:E MTAB 8958:Sample 5\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:il4/13a / \|organism part:gill\|sample name:E MTAB 8958:Sample 5\|scientific name:Danio rerio	Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills	E MTAB 8958:Sample 5 p	Sample 5 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:il4/13a /	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	FB9_S46_R1_001.fastq.gz FB9_S46_R2_001.fastq.gz	fastq fastq	4267946165.0	28455064.0	E MTAB 8958:FB9 S46 R	0:75.00 1:74.99	A:1108310330;C:999732020;G:987857724;T:1148193980;N:23852111	75	74	1108310330	999732020	987857724	1148193980	23852111	ERX4030560	ERS4514113	ERA2508092	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	2	0.9223	0.91737	0.09304	0.09006	0.69063	0.6929	0.48978	0.49675	76	75	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
9858	9858	ERR4029243	ERX4030559	ERS4514112	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 9	SAMEA6786433	UNIVERSITY OF MANCHESTER	ENA FIRST PUBLIC:2020 05 28T17:07:47Z\|ENA LAST UPDATE:2020 04 16T14:58:14Z\|External Id:SAMEA6786433\|INSDC center name:UNIVERSITY OF MANCHESTER\|INSDC first public:2020 05 28T17:07:47Z\|INSDC last update:2020 04 16T14:58:14Z\|INSDC status:public\|Submitter Id:E MTAB 8958:Sample 9\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:il10 / \|organism part:gill\|sample name:E MTAB 8958:Sample 9\|scientific name:Danio rerio	Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills	E MTAB 8958:Sample 9 p	Sample 9 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:il10 /	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	FB17_S54_R1_001.fastq.gz FB17_S54_R2_001.fastq.gz	fastq fastq	3847723303.0	25764874.0	E MTAB 8958:FB17 S54 R	0:74.65 1:74.69	A:1009950686;C:883047473;G:885821368;T:1035313325;N:33590451	74	74	1009950686	883047473	885821368	1035313325	33590451	ERX4030559	ERS4514112	ERA2508092	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	2	0.91088	0.90785	0.09899	0.09623	0.68822	0.69055	0.48686	0.49337	76	75	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
9859	9859	ERR4029242	ERX4030558	ERS4514111	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 12	SAMEA6786432	UNIVERSITY OF MANCHESTER	ENA FIRST PUBLIC:2020 05 28T17:07:47Z\|ENA LAST UPDATE:2020 04 16T14:58:14Z\|External Id:SAMEA6786432\|INSDC center name:UNIVERSITY OF MANCHESTER\|INSDC first public:2020 05 28T17:07:47Z\|INSDC last update:2020 04 16T14:58:14Z\|INSDC status:public\|Submitter Id:E MTAB 8958:Sample 12\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:il10 / \|organism part:gill\|sample name:E MTAB 8958:Sample 12\|scientific name:Danio rerio	Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills	E MTAB 8958:Sample 12 p	Sample 12 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:il10 /	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	FB20_S57_R1_001.fastq.gz FB20_S57_R2_001.fastq.gz	fastq fastq	4534822065.0	30209756.0	E MTAB 8958:FB20 S57 R	0:75.06 1:75.06	A:1181838544;C:1056097162;G:1066594521;T:1207484216;N:22807622	75	75	1181838544	1056097162	1066594521	1207484216	22807622	ERX4030558	ERS4514111	ERA2508092	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	2	0.91577	0.91513	0.09598	0.09473	0.68931	0.69132	0.49181	0.49786	74	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
9860	9860	ERR4029241	ERX4030557	ERS4514110	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 11	SAMEA6786431	UNIVERSITY OF MANCHESTER	ENA FIRST PUBLIC:2020 05 28T17:07:47Z\|ENA LAST UPDATE:2020 04 16T14:58:14Z\|External Id:SAMEA6786431\|INSDC center name:UNIVERSITY OF MANCHESTER\|INSDC first public:2020 05 28T17:07:47Z\|INSDC last update:2020 04 16T14:58:14Z\|INSDC status:public\|Submitter Id:E MTAB 8958:Sample 11\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:il10 / \|organism part:gill\|sample name:E MTAB 8958:Sample 11\|scientific name:Danio rerio	Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills	E MTAB 8958:Sample 11 p	Sample 11 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:il10 /	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	FB19_S56_R1_001.fastq.gz FB19_S56_R2_001.fastq.gz	fastq fastq	5070571422.0	33987501.0	E MTAB 8958:FB19 S56 R	0:74.58 1:74.61	A:1327496786;C:1163563377;G:1162870630;T:1365191685;N:51448944	74	74	1327496786	1163563377	1162870630	1365191685	51448944	ERX4030557	ERS4514110	ERA2508092	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	2	0.91091	0.91003	0.09944	0.09748	0.68745	0.69016	0.49706	0.49287	76	75	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
9861	9861	ERR4029240	ERX4030556	ERS4514109	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 10	SAMEA6786430	UNIVERSITY OF MANCHESTER	ENA FIRST PUBLIC:2020 05 28T17:07:47Z\|ENA LAST UPDATE:2020 04 16T14:58:14Z\|External Id:SAMEA6786430\|INSDC center name:UNIVERSITY OF MANCHESTER\|INSDC first public:2020 05 28T17:07:47Z\|INSDC last update:2020 04 16T14:58:14Z\|INSDC status:public\|Submitter Id:E MTAB 8958:Sample 10\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:il10 / \|organism part:gill\|sample name:E MTAB 8958:Sample 10\|scientific name:Danio rerio	Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills	E MTAB 8958:Sample 10 p	Sample 10 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:il10 /	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	FB18_S55_R1_001.fastq.gz FB18_S55_R2_001.fastq.gz	fastq fastq	4411576023.0	29389076.0	E MTAB 8958:FB18 S55 R	0:75.05 1:75.06	A:1153821133;C:1024593137;G:1029312154;T:1181989770;N:21859829	75	75	1153821133	1024593137	1029312154	1181989770	21859829	ERX4030556	ERS4514109	ERA2508092	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	UNIVERSITY OF MANCHESTER\|European Nucleotide Archive	2	0.90933	0.90999	0.09581	0.09404	0.68917	0.69199	0.49527	0.49791	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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;