metadata: run_metadata: 20 rows where experiment.library_selection = "unspecified" and tissue_curation

20 rows where experiment.library_selection = "unspecified" and tissue_curation_coarse = "Renal System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.title	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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
32162	32162	SRR29095835	SRX24619914	SRS21357066	SRP508906	PRJNA1113956	A zebrafish model of diabetic nephropathy	PRJNA1113956	Other	We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.	6 month zebrafish kidney 1	DN zebrafish	strain:zMIR/VDBP\|age:6 mpf\|dev stage:Adult\|collection date:2023 03 30\|geo loc name:Japan\|sex:not determined\|tissue:kidney\|BioSampleModel:Model organism or animal	6 month zebrafish with proteinuria kidney 4	OF 4	OF 4	6 month zebrafish with proteinuria kidney 4	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP508906	OF_4_1.fq OF_4_2.fq	fastq fastq	4377669000.0	14592230.0	OF 4 1.fq	0:150 1:150	A:1194166573;C:999239529;G:1001594280;T:1182651631;N:16987	150	150	1194166573	999239529	1001594280	1182651631	16987	SRX24619914	SRS21357066	SRA1872692	Mie Univeristy\|School of Medicine	Mie Univeristy												B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Japan	2024-05-21	Adult	Adult	Kidney	Renal System
32163	32163	SRR29095836	SRX24619913	SRS21357066	SRP508906	PRJNA1113956	A zebrafish model of diabetic nephropathy	PRJNA1113956	Other	We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.	6 month zebrafish kidney 1	DN zebrafish	strain:zMIR/VDBP\|age:6 mpf\|dev stage:Adult\|collection date:2023 03 30\|geo loc name:Japan\|sex:not determined\|tissue:kidney\|BioSampleModel:Model organism or animal	6 month zebrafish with proteinuria kidney 3	OF 3	OF 3	6 month zebrafish with proteinuria kidney 3	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP508906	OF_3_1.fq OF_3_2.fq	fastq fastq	4798165200.0	15993884.0	OF 3 1.fq	0:150 1:150	A:1290466714;C:1114007506;G:1115137813;T:1278535708;N:17459	150	150	1290466714	1114007506	1115137813	1278535708	17459	SRX24619913	SRS21357066	SRA1872692	Mie Univeristy\|School of Medicine	Mie Univeristy												B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Japan	2024-05-21	Adult	Adult	Kidney	Renal System
32164	32164	SRR29095837	SRX24619912	SRS21357066	SRP508906	PRJNA1113956	A zebrafish model of diabetic nephropathy	PRJNA1113956	Other	We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.	6 month zebrafish kidney 1	DN zebrafish	strain:zMIR/VDBP\|age:6 mpf\|dev stage:Adult\|collection date:2023 03 30\|geo loc name:Japan\|sex:not determined\|tissue:kidney\|BioSampleModel:Model organism or animal	6 month zebrafish with proteinuria kidney 2	OF 2	OF 2	6 month zebrafish with proteinuria kidney 2	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP508906	OF_2_1.fq OF_2_2.fq	fastq fastq	5661202800.0	18870676.0	OF 2 1.fq	0:150 1:150	A:1549085619;C:1287400217;G:1288853902;T:1535841249;N:21813	150	150	1549085619	1287400217	1288853902	1535841249	21813	SRX24619912	SRS21357066	SRA1872692	Mie Univeristy\|School of Medicine	Mie Univeristy												B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Japan	2024-05-21	Adult	Adult	Kidney	Renal System
32165	32165	SRR29095838	SRX24619911	SRS21357066	SRP508906	PRJNA1113956	A zebrafish model of diabetic nephropathy	PRJNA1113956	Other	We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.	6 month zebrafish kidney 1	DN zebrafish	strain:zMIR/VDBP\|age:6 mpf\|dev stage:Adult\|collection date:2023 03 30\|geo loc name:Japan\|sex:not determined\|tissue:kidney\|BioSampleModel:Model organism or animal	6 month zebrafish with proteinuria kidney 1	OF 1	OF 1	6 month zebrafish with proteinuria kidney 1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP508906	OF_1_1.fq OF_1_2.fq	fastq fastq	5957895600.0	19859652.0	OF 1 1.fq	0:150 1:150	A:1627320757;C:1359602784;G:1360982917;T:1609967331;N:21811	150	150	1627320757	1359602784	1360982917	1609967331	21811	SRX24619911	SRS21357066	SRA1872692	Mie Univeristy\|School of Medicine	Mie Univeristy												B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Japan	2024-05-21	Adult	Adult	Kidney	Renal System
32166	32166	SRR29095839	SRX24619910	SRS21357066	SRP508906	PRJNA1113956	A zebrafish model of diabetic nephropathy	PRJNA1113956	Other	We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.	6 month zebrafish kidney 1	DN zebrafish	strain:zMIR/VDBP\|age:6 mpf\|dev stage:Adult\|collection date:2023 03 30\|geo loc name:Japan\|sex:not determined\|tissue:kidney\|BioSampleModel:Model organism or animal	6 month zebrafish kidney 4	NF 6	NF 6	6 month zebrafish kidney 4	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP508906	NF_6_1.fq NF_6_2.fq	fastq fastq	5469504900.0	18231683.0	NF 6 1.fq	0:150 1:150	A:1480833386;C:1260945093;G:1261275041;T:1466430429;N:20951	150	150	1480833386	1260945093	1261275041	1466430429	20951	SRX24619910	SRS21357066	SRA1872692	Mie Univeristy\|School of Medicine	Mie Univeristy												B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Japan	2024-05-21	Adult	Adult	Kidney	Renal System
32167	32167	SRR29095840	SRX24619909	SRS21357066	SRP508906	PRJNA1113956	A zebrafish model of diabetic nephropathy	PRJNA1113956	Other	We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.	6 month zebrafish kidney 1	DN zebrafish	strain:zMIR/VDBP\|age:6 mpf\|dev stage:Adult\|collection date:2023 03 30\|geo loc name:Japan\|sex:not determined\|tissue:kidney\|BioSampleModel:Model organism or animal	6 month zebrafish kidney 3	NF 5	NF 5	6 month zebrafish kidney 3	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP508906	NF_5_1.fq NF_5_2.fq	fastq fastq	6386781900.0	21289273.0	NF 5 1.fq	0:150 1:150	A:1743273279;C:1458330156;G:1460747658;T:1724406616;N:24191	150	150	1743273279	1458330156	1460747658	1724406616	24191	SRX24619909	SRS21357066	SRA1872692	Mie Univeristy\|School of Medicine	Mie Univeristy												B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Japan	2024-05-21	Adult	Adult	Kidney	Renal System
32168	32168	SRR29095841	SRX24619908	SRS21357066	SRP508906	PRJNA1113956	A zebrafish model of diabetic nephropathy	PRJNA1113956	Other	We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.	6 month zebrafish kidney 1	DN zebrafish	strain:zMIR/VDBP\|age:6 mpf\|dev stage:Adult\|collection date:2023 03 30\|geo loc name:Japan\|sex:not determined\|tissue:kidney\|BioSampleModel:Model organism or animal	6 month zebrafish kidney 2	NF 2	NF 2	6 month zebrafish kidney 2	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP508906	NF_2_1.fq NF_2_2.fq	fastq fastq	5747851800.0	19159506.0	NF 2 1.fq	0:150 1:150	A:1564796254;C:1316015979;G:1317516650;T:1549501774;N:21143	150	150	1564796254	1316015979	1317516650	1549501774	21143	SRX24619908	SRS21357066	SRA1872692	Mie Univeristy\|School of Medicine	Mie Univeristy												B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Japan	2024-05-21	Adult	Adult	Kidney	Renal System
32169	32169	SRR29095842	SRX24619907	SRS21357066	SRP508906	PRJNA1113956	A zebrafish model of diabetic nephropathy	PRJNA1113956	Other	We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.	6 month zebrafish kidney 1	DN zebrafish	strain:zMIR/VDBP\|age:6 mpf\|dev stage:Adult\|collection date:2023 03 30\|geo loc name:Japan\|sex:not determined\|tissue:kidney\|BioSampleModel:Model organism or animal	6 month zebrafish kidney 1	NF 1	NF 1	6 month zebrafish kidney 1	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP508906	NF_1_1.fq NF_1_2.fq	fastq fastq	5369089800.0	17896966.0	NF 1 1.fq	0:150 1:150	A:1413369042;C:1273865602;G:1277141372;T:1404694133;N:19651	150	150	1413369042	1273865602	1277141372	1404694133	19651	SRX24619907	SRS21357066	SRA1872692	Mie Univeristy\|School of Medicine	Mie Univeristy												B	B	biological fallback assumption	illumina	novaseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Japan	2024-05-21	Adult	Adult	Kidney	Renal System
51854	51854	SRR8888280	SRX5674012	SRS4616291	SRP192333	PRJNA532380	Danio rerio SVCV infection	PRJNA532380	Other	Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.	RAGC2	RAGC2	strain:RAG\|isolate:5\|age:6 mpf\|dev stage:adult\|sex:pooled male and female\|tissue:kidney\|biomaterial provider:IIM\|birth date:2016\|birth location:IIM\|collected by:Patry Pereiro and Marga Alvarez\|collection date:2016\|death date:2016\|health state:control\|isolation source:RAGC2\|BioSampleModel:Model organism or animal	RAGC2	RAGC2	RAGC2	eukaryotic mRNA was extracted from total RNA using oligo dT magnetic beads and cleaved into short fragments using fragmentation buffer. A cDNA library compatible with the Illumina NGS technology was then prepared from the fragmented mRNA via reverse transcription second strand synthesis and ligation of specific adapters paired ends post cDNA purification using the QIAquick PCR Purification Kit Qiagen. The amount of cDNA in each library was quantified through spectrofluorometric analysis using the Qbit system. Next generation sequencing was performed using Illumina HiSeq 4000 technology	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP192333	RAGC2_1.fastq.gz RAGC2_2.fastq.gz	fastq fastq	9395399154.0	46511877.0	RAGC2 1.fastq.gz	0:101 1:101	A:2430769634;C:2266158952;G:2248647631;T:2449671730;N:151207	101	101	2430769634	2266158952	2248647631	2449671730	151207	SRX5674012	SRS4616291	SRA873264	IIM - CSIC\|Biotechnology and Aquaculture	IIM - CSIC	2	0.94312	0.94407	0.03436	0.0337	0.71277	0.71543	0.47608	0.48217	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Spain	2019-10-29	Adult	Adult	Kidney	Renal System
51855	51855	SRR8888281	SRX5674011	SRS4616290	SRP192333	PRJNA532380	Danio rerio SVCV infection	PRJNA532380	Other	Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.	RAGSVCV3	RAGSVCV3	strain:RAG\|isolate:12\|age:6 mpf\|dev stage:adult\|sex:pooled male and female\|tissue:kidney\|biomaterial provider:IIM\|birth date:2016\|birth location:IIM\|collected by:Patry Pereiro and Marga Alvarez\|collection date:2016\|death date:2016\|health state:SVCV infected\|isolation source:RAGSVCV3\|BioSampleModel:Model organism or animal	RAGSVCV3	RAGSVCV3	RAGSVCV3	eukaryotic mRNA was extracted from total RNA using oligo dT magnetic beads and cleaved into short fragments using fragmentation buffer. A cDNA library compatible with the Illumina NGS technology was then prepared from the fragmented mRNA via reverse transcription second strand synthesis and ligation of specific adapters paired ends post cDNA purification using the QIAquick PCR Purification Kit Qiagen. The amount of cDNA in each library was quantified through spectrofluorometric analysis using the Qbit system. Next generation sequencing was performed using Illumina HiSeq 4000 technology	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP192333	RAGSVCV3_2.fastq.gz RAGSVCV3_1.fastq.gz	fastq fastq	12326011316.0	61019858.0	RAGSVCV3 1.fastq.gz	0:101 1:101	A:3206276408;C:2959106015;G:2947858795;T:3212576687;N:193411	101	101	3206276408	2959106015	2947858795	3212576687	193411	SRX5674011	SRS4616290	SRA873264	IIM - CSIC\|Biotechnology and Aquaculture	IIM - CSIC	2	0.94868	0.95003	0.07106	0.07013	0.69996	0.70183	0.5208	0.52349	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Spain	2019-04-12	Adult	Adult	Kidney	Renal System
51856	51856	SRR8888282	SRX5674010	SRS4616289	SRP192333	PRJNA532380	Danio rerio SVCV infection	PRJNA532380	Other	Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.	RAGSVCV2	RAGSVCV2	strain:RAG\|isolate:11\|age:6 mpf\|dev stage:adult\|sex:pooled male and female\|tissue:kidney\|biomaterial provider:IIM\|birth date:2016\|birth location:IIM\|collected by:Patry Pereiro and Marga Alvarez\|collection date:2016\|death date:2016\|health state:SVCV infected\|isolation source:RAGSVCV2\|BioSampleModel:Model organism or animal	RAGSVCV2	RAGSVCV2	RAGSVCV2	eukaryotic mRNA was extracted from total RNA using oligo dT magnetic beads and cleaved into short fragments using fragmentation buffer. A cDNA library compatible with the Illumina NGS technology was then prepared from the fragmented mRNA via reverse transcription second strand synthesis and ligation of specific adapters paired ends post cDNA purification using the QIAquick PCR Purification Kit Qiagen. The amount of cDNA in each library was quantified through spectrofluorometric analysis using the Qbit system. Next generation sequencing was performed using Illumina HiSeq 4000 technology	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP192333	RAGSVCV2_2.fastq.gz RAGSVCV2_1.fastq.gz	fastq fastq	11704643156.0	57943778.0	RAGSVCV2 1.fastq.gz	0:101 1:101	A:3015845660;C:2834743361;G:2807548061;T:3046323528;N:182546	101	101	3015845660	2834743361	2807548061	3046323528	182546	SRX5674010	SRS4616289	SRA873264	IIM - CSIC\|Biotechnology and Aquaculture	IIM - CSIC	2	0.94284	0.94328	0.02706	0.02628	0.72445	0.7262	0.47928	0.47854	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Spain	2019-04-12	Adult	Adult	Kidney	Renal System
51857	51857	SRR8888283	SRX5674009	SRS4616288	SRP192333	PRJNA532380	Danio rerio SVCV infection	PRJNA532380	Other	Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.	RAGSVCV1	RAGSVCV1	strain:RAG\|isolate:10\|age:6 mpf\|dev stage:adult\|sex:pooled male and female\|tissue:kidney\|biomaterial provider:IIM\|birth date:2016\|birth location:IIM\|collected by:Patry Pereiro and Marga Alvarez\|collection date:2016\|death date:2016\|health state:SVCV infected\|isolation source:RAGSVCV1\|BioSampleModel:Model organism or animal	RAGSVCV1	RAGSVCV1	RAGSVCV1	eukaryotic mRNA was extracted from total RNA using oligo dT magnetic beads and cleaved into short fragments using fragmentation buffer. A cDNA library compatible with the Illumina NGS technology was then prepared from the fragmented mRNA via reverse transcription second strand synthesis and ligation of specific adapters paired ends post cDNA purification using the QIAquick PCR Purification Kit Qiagen. The amount of cDNA in each library was quantified through spectrofluorometric analysis using the Qbit system. Next generation sequencing was performed using Illumina HiSeq 4000 technology	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP192333	RAGSVCV1_1.fastq.gz RAGSVCV1_2.fastq.gz	fastq fastq	12762636134.0	63181367.0	RAGSVCV1 1.fastq.gz	0:101 1:101	A:3283344868;C:3096226266;G:3062694140;T:3320171386;N:199474	101	101	3283344868	3096226266	3062694140	3320171386	199474	SRX5674009	SRS4616288	SRA873264	IIM - CSIC\|Biotechnology and Aquaculture	IIM - CSIC	2	0.94662	0.94798	0.02887	0.02815	0.72456	0.7259	0.48456	0.47923	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Spain	2019-10-29	Adult	Adult	Kidney	Renal System
51858	51858	SRR8888284	SRX5674008	SRS4616287	SRP192333	PRJNA532380	Danio rerio SVCV infection	PRJNA532380	Other	Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.	WTSVCV3	WTSVCV3	strain:WT\|isolate:9\|age:6 mpf\|dev stage:adult\|sex:pooled male and female\|tissue:kidney\|biomaterial provider:IIM\|birth date:2016\|birth location:IIM\|collected by:Patry Pereiro and Marga Alvarez\|collection date:2016\|death date:2016\|health state:SVCV infected\|isolation source:WTSVCV3\|BioSampleModel:Model organism or animal	WTSVCV3	WTSVCV3	WTSVCV3	eukaryotic mRNA was extracted from total RNA using oligo dT magnetic beads and cleaved into short fragments using fragmentation buffer. A cDNA library compatible with the Illumina NGS technology was then prepared from the fragmented mRNA via reverse transcription second strand synthesis and ligation of specific adapters paired ends post cDNA purification using the QIAquick PCR Purification Kit Qiagen. The amount of cDNA in each library was quantified through spectrofluorometric analysis using the Qbit system. Next generation sequencing was performed using Illumina HiSeq 4000 technology	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP192333	WTSVCV3_2.fastq.gz WTSVCV3_1.fastq.gz	fastq fastq	8297391592.0	41076196.0	WTSVCV3 1.fastq.gz	0:101 1:101	A:2093736421;C:2051384514;G:2046522228;T:2105619408;N:129021	101	101	2093736421	2051384514	2046522228	2105619408	129021	SRX5674008	SRS4616287	SRA873264	IIM - CSIC\|Biotechnology and Aquaculture	IIM - CSIC	2	0.9378	0.94035	0.05179	0.04987	0.69049	0.69122	0.50167	0.50647	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Spain	2019-04-12	Adult	Adult	Kidney	Renal System
51859	51859	SRR8888285	SRX5674007	SRS4616286	SRP192333	PRJNA532380	Danio rerio SVCV infection	PRJNA532380	Other	Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.	RAGC1	RAGC1	strain:RAG\|isolate:4\|age:6 mpf\|dev stage:adult\|sex:pooled male and female\|tissue:kidney\|biomaterial provider:IIM\|birth date:2016\|birth location:IIM\|collected by:Patry Pereiro and Marga Alvarez\|collection date:2016\|death date:2016\|health state:control\|isolation source:RAGC1\|BioSampleModel:Model organism or animal	RAGC1	RAGC1	RAGC1	eukaryotic mRNA was extracted from total RNA using oligo dT magnetic beads and cleaved into short fragments using fragmentation buffer. A cDNA library compatible with the Illumina NGS technology was then prepared from the fragmented mRNA via reverse transcription second strand synthesis and ligation of specific adapters paired ends post cDNA purification using the QIAquick PCR Purification Kit Qiagen. The amount of cDNA in each library was quantified through spectrofluorometric analysis using the Qbit system. Next generation sequencing was performed using Illumina HiSeq 4000 technology	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP192333	RAGC1_2.fastq.gz RAGC1_1.fastq.gz	fastq fastq	10591446810.0	52432905.0	RAGC1 1.fastq.gz	0:101 1:101	A:2719048858;C:2574219136;G:2554779675;T:2743228364;N:170777	101	101	2719048858	2574219136	2554779675	2743228364	170777	SRX5674007	SRS4616286	SRA873264	IIM - CSIC\|Biotechnology and Aquaculture	IIM - CSIC	2	0.94276	0.94329	0.03961	0.03767	0.72336	0.72484	0.49382	0.5001	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Spain	2019-04-12	Adult	Adult	Kidney	Renal System
51860	51860	SRR8888286	SRX5674006	SRS4616285	SRP192333	PRJNA532380	Danio rerio SVCV infection	PRJNA532380	Other	Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.	WTC3	WTC3	strain:WT\|isolate:3\|age:6 mpf\|dev stage:adult\|sex:pooled male and female\|tissue:kidney\|biomaterial provider:IIM\|birth date:2016\|birth location:IIM\|collected by:Patry Pereiro and Marga Alvarez\|collection date:2016\|death date:2016\|health state:control\|isolation source:WTC3\|BioSampleModel:Model organism or animal	WTC3	WTC3	WTC3	eukaryotic mRNA was extracted from total RNA using oligo dT magnetic beads and cleaved into short fragments using fragmentation buffer. A cDNA library compatible with the Illumina NGS technology was then prepared from the fragmented mRNA via reverse transcription second strand synthesis and ligation of specific adapters paired ends post cDNA purification using the QIAquick PCR Purification Kit Qiagen. The amount of cDNA in each library was quantified through spectrofluorometric analysis using the Qbit system. Next generation sequencing was performed using Illumina HiSeq 4000 technology	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP192333	WTC3_2.fastq.gz WTC3_1.fastq.gz	fastq fastq	9025292734.0	44679667.0	WTC3 1.fastq.gz	0:101 1:101	A:2314042574;C:2192770761;G:2181143484;T:2337190359;N:145556	101	101	2314042574	2192770761	2181143484	2337190359	145556	SRX5674006	SRS4616285	SRA873264	IIM - CSIC\|Biotechnology and Aquaculture	IIM - CSIC	2	0.93612	0.93857	0.05162	0.04989	0.68889	0.69071	0.49093	0.48918	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Spain	2019-04-12	Adult	Adult	Kidney	Renal System
51861	51861	SRR8888287	SRX5674005	SRS4616284	SRP192333	PRJNA532380	Danio rerio SVCV infection	PRJNA532380	Other	Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.	WTC2	WTC2	strain:WT\|isolate:2\|age:6 mpf\|dev stage:adult\|sex:pooled male and female\|tissue:kidney\|biomaterial provider:IIM\|birth date:2016\|birth location:IIM\|collected by:Patry Pereiro and Marga Alvarez\|collection date:2016\|death date:2016\|health state:control\|isolation source:WTC2\|BioSampleModel:Model organism or animal	WTC2	WTC2	WTC2	eukaryotic mRNA was extracted from total RNA using oligo dT magnetic beads and cleaved into short fragments using fragmentation buffer. A cDNA library compatible with the Illumina NGS technology was then prepared from the fragmented mRNA via reverse transcription second strand synthesis and ligation of specific adapters paired ends post cDNA purification using the QIAquick PCR Purification Kit Qiagen. The amount of cDNA in each library was quantified through spectrofluorometric analysis using the Qbit system. Next generation sequencing was performed using Illumina HiSeq 4000 technology	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP192333	WTC2_2.fastq.gz WTC2_1.fastq.gz	fastq fastq	9232541906.0	45705653.0	WTC2 1.fastq.gz	0:101 1:101	A:2377508195;C:2235019239;G:2220061555;T:2399805579;N:147338	101	101	2377508195	2235019239	2220061555	2399805579	147338	SRX5674005	SRS4616284	SRA873264	IIM - CSIC\|Biotechnology and Aquaculture	IIM - CSIC	2	0.93618	0.93685	0.0348	0.03356	0.69891	0.7026	0.48034	0.47779	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Spain	2019-04-12	Adult	Adult	Kidney	Renal System
51862	51862	SRR8888288	SRX5674004	SRS4616283	SRP192333	PRJNA532380	Danio rerio SVCV infection	PRJNA532380	Other	Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.	WTC1	WTC1	strain:WT\|isolate:1\|age:6 mpf\|dev stage:adult\|sex:pooled male and female\|tissue:kidney\|biomaterial provider:IIM\|birth date:2016\|birth location:IIM\|collected by:Patry Pereiro and Marga Alvarez\|collection date:2016\|death date:2016\|health state:control\|isolation source:WTC1\|BioSampleModel:Model organism or animal	WTC1	WTC1	WTC1	eukaryotic mRNA was extracted from total RNA using oligo dT magnetic beads and cleaved into short fragments using fragmentation buffer. A cDNA library compatible with the Illumina NGS technology was then prepared from the fragmented mRNA via reverse transcription second strand synthesis and ligation of specific adapters paired ends post cDNA purification using the QIAquick PCR Purification Kit Qiagen. The amount of cDNA in each library was quantified through spectrofluorometric analysis using the Qbit system. Next generation sequencing was performed using Illumina HiSeq 4000 technology	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP192333	WTC1_2.fastq.gz WTC1_1.fastq.gz	fastq fastq	9556400022.0	47308911.0	WTC1 1.fastq.gz	0:101 1:101	A:2473901606;C:2299207567;G:2295951176;T:2487185750;N:153923	101	101	2473901606	2299207567	2295951176	2487185750	153923	SRX5674004	SRS4616283	SRA873264	IIM - CSIC\|Biotechnology and Aquaculture	IIM - CSIC	2	0.9355	0.93724	0.08445	0.08118	0.68168	0.68436	0.51588	0.51044	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Spain	2019-04-12	Adult	Adult	Kidney	Renal System
51863	51863	SRR8888289	SRX5674003	SRS4616282	SRP192333	PRJNA532380	Danio rerio SVCV infection	PRJNA532380	Other	Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.	WTSVCV2	WTSVCV2	strain:WT\|isolate:8\|age:6 mpf\|dev stage:adult\|sex:pooled male and female\|tissue:kidney\|biomaterial provider:IIM\|birth date:2016\|birth location:IIM\|collected by:Patry Pereiro and Marga Alvarez\|collection date:2016\|death date:2016\|health state:SVCV infected\|isolation source:WTSVCV2\|BioSampleModel:Model organism or animal	WTSVCV2	WTSVCV2	WTSVCV2	eukaryotic mRNA was extracted from total RNA using oligo dT magnetic beads and cleaved into short fragments using fragmentation buffer. A cDNA library compatible with the Illumina NGS technology was then prepared from the fragmented mRNA via reverse transcription second strand synthesis and ligation of specific adapters paired ends post cDNA purification using the QIAquick PCR Purification Kit Qiagen. The amount of cDNA in each library was quantified through spectrofluorometric analysis using the Qbit system. Next generation sequencing was performed using Illumina HiSeq 4000 technology	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP192333	WTSVCV2_2.fastq.gz WTSVCV2_1.fastq.gz	fastq fastq	9643862386.0	47741893.0	WTSVCV2 1.fastq.gz	0:101 1:101	A:2464153821;C:2351393654;G:2321170587;T:2506987423;N:156901	101	101	2464153821	2351393654	2321170587	2506987423	156901	SRX5674003	SRS4616282	SRA873264	IIM - CSIC\|Biotechnology and Aquaculture	IIM - CSIC	2	0.92021	0.93532	0.02161	0.0212	0.7346	0.73561	0.46187	0.45911	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Spain	2019-10-29	Adult	Adult	Kidney	Renal System
51864	51864	SRR8888290	SRX5674002	SRS4616281	SRP192333	PRJNA532380	Danio rerio SVCV infection	PRJNA532380	Other	Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.	WTSVCV1	WTSVCV1	strain:WT\|isolate:7\|age:6 mpf\|dev stage:adult\|sex:pooled male and female\|tissue:kidney\|biomaterial provider:IIM\|birth date:2016\|birth location:IIM\|collected by:Patry Pereiro and Marga Alvarez\|collection date:2016\|death date:2016\|health state:SVCV infected\|isolation source:WTSVCV1\|BioSampleModel:Model organism or animal	WTSVCV1	WTSVCV1	WTSVCV1	eukaryotic mRNA was extracted from total RNA using oligo dT magnetic beads and cleaved into short fragments using fragmentation buffer. A cDNA library compatible with the Illumina NGS technology was then prepared from the fragmented mRNA via reverse transcription second strand synthesis and ligation of specific adapters paired ends post cDNA purification using the QIAquick PCR Purification Kit Qiagen. The amount of cDNA in each library was quantified through spectrofluorometric analysis using the Qbit system. Next generation sequencing was performed using Illumina HiSeq 4000 technology	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP192333	WTSVCV1_2.fastq.gz WTSVCV1_1.fastq.gz	fastq fastq	9147739276.0	45285838.0	WTSVCV1 1.fastq.gz	0:101 1:101	A:2363980423;C:2206972687;G:2193838537;T:2382800420;N:147209	101	101	2363980423	2206972687	2193838537	2382800420	147209	SRX5674002	SRS4616281	SRA873264	IIM - CSIC\|Biotechnology and Aquaculture	IIM - CSIC	2	0.9349	0.93754	0.05387	0.05266	0.68004	0.68134	0.49403	0.49763	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Spain	2019-04-12	Adult	Adult	Kidney	Renal System
51865	51865	SRR8888291	SRX5674001	SRS4616280	SRP192333	PRJNA532380	Danio rerio SVCV infection	PRJNA532380	Other	Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.	RAGC3	RAGC3	strain:RAG\|isolate:6\|age:6 mpf\|dev stage:adult\|sex:pooled male and female\|tissue:kidney\|biomaterial provider:IIM\|birth date:2016\|birth location:IIM\|collected by:Patry Pereiro and Marga Alvarez\|collection date:2016\|death date:2016\|health state:control\|isolation source:RAGC3\|BioSampleModel:Model organism or animal	RAGC3	RAGC3	RAGC3	eukaryotic mRNA was extracted from total RNA using oligo dT magnetic beads and cleaved into short fragments using fragmentation buffer. A cDNA library compatible with the Illumina NGS technology was then prepared from the fragmented mRNA via reverse transcription second strand synthesis and ligation of specific adapters paired ends post cDNA purification using the QIAquick PCR Purification Kit Qiagen. The amount of cDNA in each library was quantified through spectrofluorometric analysis using the Qbit system. Next generation sequencing was performed using Illumina HiSeq 4000 technology	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP192333	RAGC3_2.fastq.gz RAGC3_1.fastq.gz	fastq fastq	9050252662.0	44803231.0	RAGC3 1.fastq.gz	0:101 1:101	A:2371998407;C:2151330416;G:2139236805;T:2387539526;N:147508	101	101	2371998407	2151330416	2139236805	2387539526	147508	SRX5674001	SRS4616280	SRA873264	IIM - CSIC\|Biotechnology and Aquaculture	IIM - CSIC	2	0.94456	0.94478	0.05685	0.05538	0.67793	0.6787	0.49516	0.49468	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	Spain	2019-04-12	Adult	Adult	Kidney	Renal System

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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");;