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74 rows where devstage_curation = "Adult" and experiment.library_selection = "unspecified"

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tissue_curation 7

experiment.library_strategy 3

technology 2

experiment.library_source 2

experiment.library_layout 2

experiment.platform 1

experiment.library_selection 1

  • unspecified · 74 ✖

devstage_curation_coarse 1

devstage_curation 1

  • Adult · 74 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession 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.spot_descriptor 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.r3_length run.r4_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 tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
8059 8059 ERR022480 ERX008923 ERS000088 ERP000400 PRJEB2333 Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E-MTAB-434 Other         ZF female head sample1 SAMEA708836 Wellcome Sanger Institute Alias:ZF female head sample1|Description:RNA extracted from female adult zebrafish head|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000088|Sample Name:ERS000088|Sex:female|Strain:Tuebingen|Title:Danio rerio                 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E MTAB 434:sequencing of Zebrafish adult female head RNA from Zebrafish adult female head Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C. Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 150 to 200 bp. Experimental Factor: DEVELPOMENTAL STAGE:adult|Experimental Factor: ORGANISM PART:head FL-cDNA TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer II   ERP000400 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16 2719_5.srf srf 1622590272.0 15023984.0 E MTAB 434:2719 5.srf 0:54 1:54 A:426435544;C:373743071;G:387589492;T:432086510;N:2735655 54 54     426435544 373743071 387589492 432086510 2735655 ERX008923 ERS000088 ERA015179 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.94624 0.94338 0.17949 0.17965 0.66454 0.66872 0.51097 0.51377 54 54 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United Kingdom 2010-02-26 Adult Adult Head Nervous System
8060 8060 ERR022481 ERX008923 ERS000088 ERP000400 PRJEB2333 Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E-MTAB-434 Other         ZF female head sample1 SAMEA708836 Wellcome Sanger Institute Alias:ZF female head sample1|Description:RNA extracted from female adult zebrafish head|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000088|Sample Name:ERS000088|Sex:female|Strain:Tuebingen|Title:Danio rerio                 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E MTAB 434:sequencing of Zebrafish adult female head RNA from Zebrafish adult female head Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C. Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 150 to 200 bp. Experimental Factor: DEVELPOMENTAL STAGE:adult|Experimental Factor: ORGANISM PART:head FL-cDNA TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer II   ERP000400 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16 2719_6.srf srf 1693460736.0 15680192.0 E MTAB 434:2719 6.srf 0:54 1:54 A:445666325;C:389360280;G:403789644;T:451529226;N:3115261 54 54     445666325 389360280 403789644 451529226 3115261 ERX008923 ERS000088 ERA015179 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.94579 0.94429 0.17895 0.17923 0.66864 0.67164 0.51788 0.51083 54 54 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United Kingdom 2010-02-26 Adult Adult Head Nervous System
9982 9982 ERR4568390 ERX4504063 ERS5050806 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Proximal Rep3 SAMEA7292236 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292236|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Proximal Rep3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Proximal Rep3|sampling site:proximal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Proximal Rep3 p HypoTH Proximal Rep3 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:proximal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HP3_CRRA200004859-1a_HV532DSXX_L4_1.fq.gz HP3_CRRA200004859-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7117020000.0 23723400.0 E MTAB 9528:HP3 CRRA200004859 1a HV532DSXX L4 0:150 1:150 A:1864896771;C:1704008842;G:1704487221;T:1843451594;N:175572 150 150     1864896771 1704008842 1704487221 1843451594 175572 ERX4504063 ERS5050806 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.94335 0.9433 0.08657 0.08625 0.72498 0.72636 0.48274 0.4859 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9983 9983 ERR4568389 ERX4504062 ERS5050805 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Proximal Rep2 SAMEA7292235 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292235|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Proximal Rep2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Proximal Rep2|sampling site:proximal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Proximal Rep2 p HypoTH Proximal Rep2 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:proximal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HP2_CRRA200004858-1a_HV532DSXX_L4_1.fq.gz HP2_CRRA200004858-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7810736700.0 26035789.0 E MTAB 9528:HP2 CRRA200004858 1a HV532DSXX L4 0:150 1:150 A:2064202307;C:1840783570;G:1863746983;T:2041812726;N:191114 150 150     2064202307 1840783570 1863746983 2041812726 191114 ERX4504062 ERS5050805 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93642 0.93627 0.08781 0.08757 0.72841 0.72872 0.48431 0.48311 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9984 9984 ERR4568388 ERX4504061 ERS5050804 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Proximal Rep1 SAMEA7292234 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292234|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Proximal Rep1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Proximal Rep1|sampling site:proximal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Proximal Rep1 p HypoTH Proximal Rep1 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:proximal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HP1_CRRA200004857-1a_HV532DSXX_L4_1.fq.gz HP1_CRRA200004857-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7143318600.0 23811062.0 E MTAB 9528:HP1 CRRA200004857 1a HV532DSXX L4 0:150 1:150 A:1883244963;C:1695388732;G:1697412462;T:1867096015;N:176428 150 150     1883244963 1695388732 1697412462 1867096015 176428 ERX4504061 ERS5050804 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.9408 0.94186 0.08491 0.08465 0.73129 0.73099 0.47185 0.47442 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9985 9985 ERR4568387 ERX4504060 ERS5050803 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Proximal Rep3 SAMEA7292233 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292233|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Proximal Rep3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Proximal Rep3|sampling site:proximal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Proximal Rep3 p EuTH Proximal Rep3 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:proximal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 EP3_CRRA200004850-1a_HV532DSXX_L4_1.fq.gz EP3_CRRA200004850-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7860809700.0 26202699.0 E MTAB 9528:EP3 CRRA200004850 1a HV532DSXX L4 0:150 1:150 A:2068735854;C:1871645002;G:1876330645;T:2043901317;N:196882 150 150     2068735854 1871645002 1876330645 2043901317 196882 ERX4504060 ERS5050803 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93854 0.93903 0.09256 0.09314 0.74014 0.74059 0.47935 0.47779 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9986 9986 ERR4568386 ERX4504059 ERS5050802 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Proximal Rep2 SAMEA7292232 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292232|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Proximal Rep2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Proximal Rep2|sampling site:proximal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Proximal Rep2 p EuTH Proximal Rep2 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:proximal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 EP2_CRRA200004849-1a_HV532DSXX_L4_1.fq.gz EP2_CRRA200004849-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7168033200.0 23893444.0 E MTAB 9528:EP2 CRRA200004849 1a HV532DSXX L4 0:150 1:150 A:1903193161;C:1689671926;G:1689805787;T:1885183061;N:179265 150 150     1903193161 1689671926 1689805787 1885183061 179265 ERX4504059 ERS5050802 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93988 0.93957 0.08429 0.08448 0.74399 0.74375 0.4672 0.47077 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9987 9987 ERR4568385 ERX4504058 ERS5050801 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Proximal Rep1 SAMEA7292231 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292231|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Proximal Rep1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Proximal Rep1|sampling site:proximal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Proximal Rep1 p EuTH Proximal Rep1 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:proximal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 EP1_CRRA200004848-1a_HV532DSXX_L4_1.fq.gz EP1_CRRA200004848-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7993254600.0 26644182.0 E MTAB 9528:EP1 CRRA200004848 1a HV532DSXX L4 0:150 1:150 A:2055964917;C:1952736981;G:1951688671;T:2032664860;N:199171 150 150     2055964917 1952736981 1951688671 2032664860 199171 ERX4504058 ERS5050801 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.94523 0.94513 0.09369 0.09348 0.74511 0.74525 0.48633 0.48842 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9988 9988 ERR4568384 ERX4504057 ERS5050800 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Middle Rep3 SAMEA7292230 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292230|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Middle Rep3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Middle Rep3|sampling site:middle portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Middle Rep3 p HypoTH Middle Rep3 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:middle portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HM3_CRRA200004862-1a_HV532DSXX_L4_1.fq.gz HM3_CRRA200004862-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7418093400.0 24726978.0 E MTAB 9528:HM3 CRRA200004862 1a HV532DSXX L4 0:150 1:150 A:1979368375;C:1736175227;G:1747418895;T:1954949103;N:181800 150 150     1979368375 1736175227 1747418895 1954949103 181800 ERX4504057 ERS5050800 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93389 0.93398 0.0839 0.08406 0.72147 0.72115 0.47407 0.47898 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9989 9989 ERR4568383 ERX4504056 ERS5050799 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Middle Rep2 SAMEA7292229 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292229|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Middle Rep2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Middle Rep2|sampling site:middle portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Middle Rep2 p HypoTH Middle Rep2 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:middle portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HM2_CRRA200004861-1a_HV532DSXX_L4_1.fq.gz HM2_CRRA200004861-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7047855300.0 23492851.0 E MTAB 9528:HM2 CRRA200004861 1a HV532DSXX L4 0:150 1:150 A:1909885369;C:1626900113;G:1623501695;T:1887391464;N:176659 150 150     1909885369 1626900113 1623501695 1887391464 176659 ERX4504056 ERS5050799 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93212 0.93173 0.08713 0.08625 0.7136 0.71411 0.47182 0.46635 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9990 9990 ERR4568382 ERX4504055 ERS5050798 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Middle Rep1 SAMEA7292228 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292228|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Middle Rep1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Middle Rep1|sampling site:middle portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Middle Rep1 p HypoTH Middle Rep1 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:middle portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HM1_CRRA200004860-1a_HV532DSXX_L4_1.fq.gz HM1_CRRA200004860-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7368139500.0 24560465.0 E MTAB 9528:HM1 CRRA200004860 1a HV532DSXX L4 0:150 1:150 A:1979116696;C:1681144383;G:1748755925;T:1958940264;N:182232 150 150     1979116696 1681144383 1748755925 1958940264 182232 ERX4504055 ERS5050798 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.90037 0.90035 0.07933 0.07951 0.72547 0.72512 0.46313 0.45076 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9991 9991 ERR4568381 ERX4504054 ERS5050797 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Middle Rep3 SAMEA7292227 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292227|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Middle Rep3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Middle Rep3|sampling site:middle portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Middle Rep3 p EuTH Middle Rep3 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:middle portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 EM3_CRRA200004853-1a_HV532DSXX_L4_1.fq.gz EM3_CRRA200004853-1a_HV532DSXX_L4_2.fq.gz fastq fastq 8203926600.0 27346422.0 E MTAB 9528:EM3 CRRA200004853 1a HV532DSXX L4 0:150 1:150 A:2145970242;C:1969430575;G:1966154582;T:2122170071;N:201130 150 150     2145970242 1969430575 1966154582 2122170071 201130 ERX4504054 ERS5050797 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.9358 0.93551 0.11154 0.11215 0.73908 0.73813 0.50711 0.50991 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9992 9992 ERR4568380 ERX4504053 ERS5050796 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Middle Rep2 SAMEA7292226 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292226|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Middle Rep2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Middle Rep2|sampling site:middle portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Middle Rep2 p EuTH Middle Rep2 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:middle portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 EM2_CRRA200004852-1a_HV532DSXX_L4_1.fq.gz EM2_CRRA200004852-1a_HV532DSXX_L4_2.fq.gz fastq fastq 8189085300.0 27296951.0 E MTAB 9528:EM2 CRRA200004852 1a HV532DSXX L4 0:150 1:150 A:2190135788;C:1917852780;G:1910200259;T:2170694756;N:201717 150 150     2190135788 1917852780 1910200259 2170694756 201717 ERX4504053 ERS5050796 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93471 0.93387 0.0982 0.0981 0.73357 0.73401 0.47523 0.47764 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9993 9993 ERR4568379 ERX4504052 ERS5050795 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Middle Rep1 SAMEA7292225 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292225|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Middle Rep1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Middle Rep1|sampling site:middle portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Middle Rep1 p EuTH Middle Rep1 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:middle portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 EM1_CRRA200004851-1a_HV532DSXX_L4_1.fq.gz EM1_CRRA200004851-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7099416900.0 23664723.0 E MTAB 9528:EM1 CRRA200004851 1a HV532DSXX L4 0:150 1:150 A:1906046714;C:1656677333;G:1651795527;T:1884722014;N:175312 150 150     1906046714 1656677333 1651795527 1884722014 175312 ERX4504052 ERS5050795 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93383 0.93423 0.08879 0.08881 0.73699 0.73669 0.47814 0.47895 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9994 9994 ERR4568378 ERX4504051 ERS5050794 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Distal Rep3 SAMEA7292224 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292224|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Distal Rep3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Distal Rep3|sampling site:distal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Distal Rep3 p HypoTH Distal Rep3 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:distal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HD3_CRRA200004865-1a_HV532DSXX_L4_1.fq.gz HD3_CRRA200004865-1a_HV532DSXX_L4_2.fq.gz fastq fastq 8040672900.0 26802243.0 E MTAB 9528:HD3 CRRA200004865 1a HV532DSXX L4 0:150 1:150 A:2167099154;C:1865357004;G:1864002622;T:2144021108;N:193012 150 150     2167099154 1865357004 1864002622 2144021108 193012 ERX4504051 ERS5050794 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.92854 0.92899 0.09996 0.09934 0.71902 0.71881 0.4815 0.47867 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9995 9995 ERR4568377 ERX4504050 ERS5050793 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Distal Rep2 SAMEA7292223 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292223|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Distal Rep2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Distal Rep2|sampling site:distal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Distal Rep2 p HypoTH Distal Rep2 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:distal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HD2_CRRA200004864-1a_HV532DSXX_L4_1.fq.gz HD2_CRRA200004864-1a_HV532DSXX_L4_2.fq.gz fastq fastq 8313797700.0 27712659.0 E MTAB 9528:HD2 CRRA200004864 1a HV532DSXX L4 0:150 1:150 A:2273004120;C:1900982980;G:1898877384;T:2240725057;N:208159 150 150     2273004120 1900982980 1898877384 2240725057 208159 ERX4504050 ERS5050793 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.92628 0.92613 0.09471 0.09395 0.72003 0.72054 0.47995 0.47659 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9996 9996 ERR4568376 ERX4504049 ERS5050792 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Distal Rep1 SAMEA7292222 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292222|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Distal Rep1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Distal Rep1|sampling site:distal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Distal Rep1 p HypoTH Distal Rep1 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:distal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HD1_CRRA200004863-1a_HV532DSXX_L4_1.fq.gz HD1_CRRA200004863-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7169598300.0 23898661.0 E MTAB 9528:HD1 CRRA200004863 1a HV532DSXX L4 0:150 1:150 A:1941925699;C:1655391745;G:1656382398;T:1915720427;N:178031 150 150     1941925699 1655391745 1656382398 1915720427 178031 ERX4504049 ERS5050792 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.92656 0.92587 0.09244 0.09155 0.72537 0.72577 0.483 0.48459 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9997 9997 ERR4568375 ERX4504048 ERS5050791 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Distal Rep3 SAMEA7292221 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292221|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Distal Rep3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Distal Rep3|sampling site:distal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Distal Rep3 p EuTH Distal Rep3 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:distal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 ED3_CRRA200004856-1a_HV532DSXX_L4_1.fq.gz ED3_CRRA200004856-1a_HV532DSXX_L4_2.fq.gz fastq fastq 8216298900.0 27387663.0 E MTAB 9528:ED3 CRRA200004856 1a HV532DSXX L4 0:150 1:150 A:2202070307;C:1915188230;G:1918164478;T:2180672072;N:203813 150 150     2202070307 1915188230 1918164478 2180672072 203813 ERX4504048 ERS5050791 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93043 0.92995 0.07828 0.07796 0.73799 0.73912 0.46784 0.47067 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9998 9998 ERR4568374 ERX4504047 ERS5050790 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Distal Rep2 SAMEA7292220 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292220|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Distal Rep2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Distal Rep2|sampling site:distal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Distal Rep2 p EuTH Distal Rep2 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:distal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 ED2_CRRA200004855-1a_HV532DSXX_L4_1.fq.gz ED2_CRRA200004855-1a_HV532DSXX_L4_2.fq.gz fastq fastq 6629601000.0 22098670.0 E MTAB 9528:ED2 CRRA200004855 1a HV532DSXX L4 0:150 1:150 A:1741036830;C:1583210201;G:1581636803;T:1723551874;N:165292 150 150     1741036830 1583210201 1581636803 1723551874 165292 ERX4504047 ERS5050790 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93472 0.93506 0.0948 0.09463 0.75235 0.75235 0.49522 0.49267 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9999 9999 ERR4568373 ERX4504046 ERS5050789 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Distal Rep1 SAMEA7292219 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292219|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Distal Rep1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Distal Rep1|sampling site:distal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Distal Rep1 p EuTH Distal Rep1 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:distal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 ED1_CRRA200004854-1a_HV532DSXX_L4_1.fq.gz ED1_CRRA200004854-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7261648200.0 24205494.0 E MTAB 9528:ED1 CRRA200004854 1a HV532DSXX L4 0:150 1:150 A:1943655774;C:1694798398;G:1699834504;T:1923179081;N:180443 150 150     1943655774 1694798398 1699834504 1923179081 180443 ERX4504046 ERS5050789 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.92967 0.92953 0.08728 0.08781 0.73819 0.73797 0.49368 0.49233 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
10056 10056 ERR4691987 ERX4613068 ERS5216074 ERP124560 PRJEB40865 RNA seq of zebrafish adult MCU mutant hearts ena-STUDY-UCLA-16-10-2020-22:30:44:295-390 Other We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart. ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16     zebrafish adult heart RNA SAMEA7457891 UCLA ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457891|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:mcu mutant 2|common name:zebrafish|dev stage:adult|sample name:mcu mutant 2|scientific name:Danio rerio|tissue type:heart                 Illumina HiSeq 3000 sequencing ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 4 unspecified 1     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 3000   ERP124560 Illumina HiSeq 3000 sequencing ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21 MCU_2.fastq.gz fastq 1291626898.0 35072619.0 ena RUN UCLA 16 10 2020 22:30:43:819 4 0:36.83 1:0 A:364596432;C:305716590;G:295397140;T:324498501;N:1418235 36 0     364596432 305716590 295397140 324498501 1418235 ERX4613068 ERS5216074 ERA2987364 European Nucleotide Archive University of California, Los Angeles, USA 1 0.93311   0.08182   0.75852   0.54813   37   B   usable mapping rate illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2020-10-16 Adult Adult Heart Cardiovascular System
10057 10057 ERR4691986 ERX4613067 ERS5216073 ERP124560 PRJEB40865 RNA seq of zebrafish adult MCU mutant hearts ena-STUDY-UCLA-16-10-2020-22:30:44:295-390 Other We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart. ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16     zebrafish adult heart RNA SAMEA7457890 UCLA ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457890|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:mcu mutant 1|common name:zebrafish|dev stage:adult|sample name:mcu mutant 1|scientific name:Danio rerio|tissue type:heart                 Illumina HiSeq 3000 sequencing ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 3 unspecified 1     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 3000   ERP124560 Illumina HiSeq 3000 sequencing ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21 MCU_1.fastq.gz fastq 1236033124.0 33559740.0 ena RUN UCLA 16 10 2020 22:30:43:819 3 0:36.83 1:0 A:348518065;C:293502111;G:279181983;T:313506799;N:1324166 36 0     348518065 293502111 279181983 313506799 1324166 ERX4613067 ERS5216073 ERA2987364 European Nucleotide Archive University of California, Los Angeles, USA 1 0.92798   0.07907   0.7697   0.5488   37   B   usable mapping rate illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2020-10-16 Adult Adult Heart Cardiovascular System
10058 10058 ERR4691985 ERX4613066 ERS5216072 ERP124560 PRJEB40865 RNA seq of zebrafish adult MCU mutant hearts ena-STUDY-UCLA-16-10-2020-22:30:44:295-390 Other We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart. ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16     zebrafish adult heart RNA SAMEA7457889 UCLA ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457889|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:wildtype 2|common name:zebrafish|dev stage:adult|sample name:wildtype 2|scientific name:Danio rerio|tissue type:heart                 Illumina HiSeq 3000 sequencing ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 3000   ERP124560 Illumina HiSeq 3000 sequencing ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21 WT_2.fastq.gz fastq 1180831209.0 32069533.0 ena RUN UCLA 16 10 2020 22:30:43:819 2 0:36.82 1:0 A:328604642;C:281065336;G:278743466;T:291039015;N:1378750 36 0     328604642 281065336 278743466 291039015 1378750 ERX4613066 ERS5216072 ERA2987364 European Nucleotide Archive University of California, Los Angeles, USA 1 0.92319   0.08946   0.75706   0.49996   37   B   usable mapping rate illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2020-10-16 Adult Adult Heart Cardiovascular System
10059 10059 ERR4691984 ERX4613065 ERS5216071 ERP124560 PRJEB40865 RNA seq of zebrafish adult MCU mutant hearts ena-STUDY-UCLA-16-10-2020-22:30:44:295-390 Other We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart. ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16     zebrafish adult heart RNA SAMEA7457888 UCLA ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457888|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:wildtype 1|common name:zebrafish|dev stage:adult|sample name:wildtype 1|scientific name:Danio rerio|tissue type:heart                 Illumina HiSeq 3000 sequencing ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 3000   ERP124560 Illumina HiSeq 3000 sequencing ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21 WT_1.fastq.gz fastq 1428414407.0 38793098.0 ena RUN UCLA 16 10 2020 22:30:43:819 1 0:36.82 1:0 A:398925739;C:338731211;G:333527196;T:355553981;N:1676280 36 0     398925739 338731211 333527196 355553981 1676280 ERX4613065 ERS5216071 ERA2987364 European Nucleotide Archive University of California, Los Angeles, USA 1 0.92407   0.08758   0.75726   0.4969   37   B   usable mapping rate illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2020-10-16 Adult Adult Heart Cardiovascular System
25302 25302 SRR25793493 SRX21515745 SRS18742910 SRP457465 PRJNA1010662 The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis. PRJNA1010662 Other Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.       Single cell Pr1phros ADULT miR 144 mutant Danio rerio miR 144   isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:blood|BioSampleModel:Model organism or animal                 Single cell Pr1phros ADULT miR 144 mutant Danio rerio CD 144 1 CD 144 1 Single cell library cloning was done with 10X Genomics     RNA-Seq TRANSCRIPTOMIC SINGLE CELL unspecified PAIRED ILLUMINA NextSeq 2000   SRP457465     CD_144_1_S3_R1.fastq CD_144_1_S3_R2.fastq fastq fastq 12899093774.0 108395746.0 CD 144 1 S3 R1.fastq 0:28 1:91 A:3225260764;C:3211986177;G:3151471558;T:3308055659;N:2319616 28 91     3225260764 3211986177 3151471558 3308055659 2319616 SRX21515745 SRS18742910 SRA1701829 University of East Anglia|Biological Sciences University of East Anglia 2 0.00483 0.97382 0.00157 0.05913 0.99439 0.86815 0.46634 0.45907 28 91 T B sc-like readlen illumina nextseq_v2 unknown unknown unknown sc single_cell_droplet 10x   United Kingdom 2023-08-30 Adult Adult Blood Hematopoietic System
25303 25303 SRR25793494 SRX21515744 SRS18742909 SRP457465 PRJNA1010662 The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis. PRJNA1010662 Other Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.       Single cell Pr1phros ADULT Wild type Danio rerio WT   isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:blood|BioSampleModel:Model organism or animal                 Single cell Pr1phros ADULT Wild type Danio rerio CD wt 1 CD wt 1 Single cell library cloning was done with 10X Genomics     RNA-Seq TRANSCRIPTOMIC SINGLE CELL unspecified PAIRED ILLUMINA NextSeq 2000   SRP457465     CD_wt_1_S2_R1.fastq CD_wt_1_S2_R2.fastq fastq fastq 12715533299.0 106853221.0 CD wt 1 S2 R1.fastq 0:28 1:91 A:3324705878;C:3042843364;G:3105568183;T:3240105528;N:2310346 28 91     3324705878 3042843364 3105568183 3240105528 2310346 SRX21515744 SRS18742909 SRA1701829 University of East Anglia|Biological Sciences University of East Anglia 2 0.00593 0.93177 0.00191 0.09596 0.99257 0.84394 0.42447 0.4869 28 91 T B sc-like readlen illumina nextseq_v2 unknown unknown unknown sc single_cell_droplet 10x   United Kingdom 2023-08-30 Adult Adult Blood Hematopoietic System
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
37921 37921 SRR1554495 SRX685396 SRS686645 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF4Ovary1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Ovary2 ZF4Ovary2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF4_Ovary_3.fq.gz fastq 1225610154.0 12134754.0 Ovary2 Run3 0:101 A:347141358;C:303255805;G:280185540;T:294456010;N:571441 101       347141358 303255805 280185540 294456010 571441 SRX685396 SRS686645 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 2e-05   1e-05   1.0       101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37922 37922 SRR1554492 SRX685395 SRS686644 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF2Testis1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Testis2 ZF2Testis2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF2_Testis_3.fq.gz fastq 1192024422.0 11802222.0 Testis2 Run3 0:101 A:373380865;C:276125943;G:251033102;T:290931637;N:552875 101       373380865 276125943 251033102 290931637 552875 SRX685395 SRS686644 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 3e-05   1e-05   0.99997   0.0   101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37923 37923 SRR1554489 SRX685394 SRS686642 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF2Heart1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97408|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Heart2 ZF2Heart2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF2_Heart_3.fq.gz fastq 1302765670.0 12898670.0 Heart2 Run3 0:101 A:397689061;C:312745449;G:268626802;T:323141419;N:562939 101       397689061 312745449 268626802 323141419 562939 SRX685394 SRS686642 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 3e-05   2e-05   0.99997   1.0   101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Heart Cardiovascular System
37924 37924 SRR1554486 SRX685392 SRS686641 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF2Brain1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97407|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Brain2 ZF2Brain2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF2_Brain_3.fq.gz fastq 1211892536.0 11998936.0 Brain2 Run3 0:101 A:374228993;C:286134640;G:253944548;T:297038575;N:545780 101       374228993 286134640 253944548 297038575 545780 SRX685392 SRS686641 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.0   0.0   1.0       101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Brain Nervous System
37925 37925 SRR1554483 SRX685391 SRS686559 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF3Ovary1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Ovary1 ZF3Ovary2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF3_Ovary_3.fq.gz fastq 347516154.0 3440754.0 Ovary1 Run3 0:101 A:107805981;C:80183725;G:73617313;T:85763181;N:145954 101       107805981 80183725 73617313 85763181 145954 SRX685391 SRS686559 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 5e-05   4e-05   1.0       101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37926 37926 SRR1554480 SRX685390 SRS686542 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF1Testis1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Testis1 ZF1Testis2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF1_Testis_3.fq.gz fastq 1184228636.0 11725036.0 Testis1 Run3 0:101 A:340636900;C:278505979;G:259975802;T:304564724;N:545231 101       340636900 278505979 259975802 304564724 545231 SRX685390 SRS686542 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 1e-05   0.0   1.0       101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37927 37927 SRR1554477 SRX685389 SRS566618 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF1Heart1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97404|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish individual 1 heart ZF1Heart2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF1_Heart_3.fq.gz fastq 1561371524.0 15459124.0 Heart1 Run3 0:101 A:454757966;C:391143691;G:334715236;T:380114024;N:640607 101       454757966 391143691 334715236 380114024 640607 SRX685389 SRS566618 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 3e-05   2e-05   0.99997   1.0   101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Heart Cardiovascular System
37928 37928 SRR1554474 SRX685388 SRS566490 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF1Brain1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97403|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Brain1 ZFBrain1 2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF1_Brain_3.fq.gz fastq 1192445794.0 11806394.0 Brain1 Run3 0:101 A:369786121;C:268557682;G:265557417;T:288006805;N:537769 101       369786121 268557682 265557417 288006805 537769 SRX685388 SRS566490 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 2e-05   1e-05   1.0       101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Brain Nervous System
37929 37929 SRR1554493 SRX683354 SRS686645 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF4Ovary1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Ovary2 ZF4Ovary1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF4_Ovary_1.fq.gz fastq 476104278.0 9335378.0 Ovary2 Run1 0:51 A:111060704;C:120863975;G:129849761;T:114224677;N:105161 51       111060704 120863975 129849761 114224677 105161 SRX683354 SRS686645 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.00027   8e-05   0.99945   0.8125   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37930 37930 SRR1554494 SRX683354 SRS686645 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF4Ovary1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Ovary2 ZF4Ovary1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF4_Ovary_2.fq.gz fastq 561956352.0 11018752.0 Ovary2 Run2 0:51 A:129925815;C:148479658;G:148478706;T:132824290;N:2247883 51       129925815 148479658 148478706 132824290 2247883 SRX683354 SRS686645 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.00022   0.0001   0.99967   0.6875   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37931 37931 SRR1554490 SRX683353 SRS686644 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF2Testis1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Testis2 ZF2Testis1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF2_Testis_1.fq.gz fastq 586152231.0 11493181.0 Testis2 Run1 0:51 A:145360493;C:148943988;G:151402108;T:140286245;N:159397 51       145360493 148943988 151402108 140286245 159397 SRX683353 SRS686644 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 8e-05   2e-05   0.99985   0.57142   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37932 37932 SRR1554491 SRX683353 SRS686644 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF2Testis1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Testis2 ZF2Testis1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF2_Testis_2.fq.gz fastq 697016337.0 13666987.0 Testis2 Run2 0:51 A:172082858;C:184634425;G:173370430;T:163527914;N:3400710 51       172082858 184634425 173370430 163527914 3400710 SRX683353 SRS686644 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 8e-05   2e-05   0.99985   0.57142   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37933 37933 SRR1554487 SRX683351 SRS686642 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF2Heart1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97408|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Heart2 ZF2Heart1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF2_Heart_1.fq.gz fastq 767836212.0 15055612.0 Heart2 Run1 0:51 A:192620363;C:202013249;G:191038597;T:181862075;N:301928 51       192620363 202013249 191038597 181862075 301928 SRX683351 SRS686642 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 5e-05   3e-05   0.99995   1.0   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Heart Cardiovascular System
37934 37934 SRR1554488 SRX683351 SRS686642 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF2Heart1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97408|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Heart2 ZF2Heart1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF2_Heart_2.fq.gz fastq 979886205.0 19213455.0 Heart2 Run2 0:51 A:246169086;C:264387065;G:236377487;T:227289693;N:5662874 51       246169086 264387065 236377487 227289693 5662874 SRX683351 SRS686642 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 2e-05   0.0   1.0       51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Heart Cardiovascular System
37935 37935 SRR1554484 SRX683268 SRS686641 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF2Brain1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97407|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Brain2 ZF2Brain1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF2_Brain_1.fq.gz fastq 654412671.0 12831621.0 Brain2 Run1 0:51 A:160544180;C:166355290;G:168608762;T:158684308;N:220131 51       160544180 166355290 168608762 158684308 220131 SRX683268 SRS686641 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 3e-05   0.0   0.99993   1.0   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Brain Nervous System
37936 37936 SRR1554485 SRX683268 SRS686641 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF2Brain1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97407|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Brain2 ZF2Brain1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF2_Brain_2.fq.gz fastq 856322793.0 16790643.0 Brain2 Run2 0:51 A:210706815;C:226772546;G:212404752;T:201722093;N:4716587 51       210706815 226772546 212404752 201722093 4716587 SRX683268 SRS686641 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.0   0.0   1.0       51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Brain Nervous System
37937 37937 SRR1554481 SRX683080 SRS686559 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF3Ovary1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Ovary1 ZF3Ovary1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF3_Ovary_1.fq.gz fastq 116086965.0 2276215.0 Ovary1 Run1 0:51 A:29237121;C:30235277;G:29264328;T:27320814;N:29425 51       29237121 30235277 29264328 27320814 29425 SRX683080 SRS686559 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.00022   9e-05   0.99967   0.65   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37938 37938 SRR1554482 SRX683080 SRS686559 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF3Ovary1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Ovary1 ZF3Ovary1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF3_Ovary_2.fq.gz fastq 138905844.0 2723644.0 Ovary1 Run2 0:51 A:34695180;C:38015933;G:33434207;T:32057083;N:703441 51       34695180 38015933 33434207 32057083 703441 SRX683080 SRS686559 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.00016   5e-05   0.99977   0.42857   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37939 37939 SRR1554478 SRX683062 SRS686542 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF1Testis1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Testis1 ZF1Testis1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF1_Testis_1.fq.gz fastq 655515750.0 12853250.0 Testis1 Run1 0:51 A:152422885;C:163771947;G:179144090;T:159997538;N:179290 51       152422885 163771947 179144090 159997538 179290 SRX683062 SRS686542 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.0011   0.00053   0.99829   0.67777   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37940 37940 SRR1554479 SRX683062 SRS686542 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF1Testis1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Testis1 ZF1Testis1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF1_Testis_2.fq.gz fastq 777594399.0 15246949.0 Testis1 Run2 0:51 A:180116528;C:202508153;G:204833105;T:186435696;N:3700917 51       180116528 202508153 204833105 186435696 3700917 SRX683062 SRS686542 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.00073   0.00032   0.99898   0.62745   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37941 37941 SRR1554475 SRX482035 SRS566618 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF1Heart1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97404|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish individual 1 heart ZF1Heart1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF1_Heart_1.fq.gz fastq 810162642.0 15885542.0 Heart1 Run1 0:51 A:199665102;C:213941735;G:204361738;T:191870055;N:324012 51       199665102 213941735 204361738 191870055 324012 SRX482035 SRS566618 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 6e-05   1e-05   0.99989   0.8   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Heart Cardiovascular System
37942 37942 SRR1554476 SRX482035 SRS566618 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF1Heart1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97404|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish individual 1 heart ZF1Heart1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF1_Heart_2.fq.gz fastq 1013563698.0 19873798.0 Heart1 Run2 0:51 A:249913434;C:275453651;G:247166233;T:235034199;N:5996181 51       249913434 275453651 247166233 235034199 5996181 SRX482035 SRS566618 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 4e-05   2e-05   0.99997   0.0   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Heart Cardiovascular System
37943 37943 SRR1554472 SRX481992 SRS566490 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF1Brain1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97403|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Brain1 ZFBrain1 1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF1_Brain_1.fq.gz fastq 679860294.0 13330594.0 Brain1 Run1 0:51 A:167202435;C:176450132;G:174468721;T:161497185;N:241821 51       167202435 176450132 174468721 161497185 241821 SRX481992 SRS566490 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.0   0.0   1.0       51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Brain Nervous System
37944 37944 SRR1554473 SRX481992 SRS566490 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF1Brain1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97403|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Brain1 ZFBrain1 1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF1_Brain_2.fq.gz fastq 838372782.0 16438682.0 Brain1 Run2 0:51 A:206906228;C:221202670;G:210716690;T:195319694;N:4227500 51       206906228 221202670 210716690 195319694 4227500 SRX481992 SRS566490 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.0   0.0   1.0       51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Brain Nervous System
39636 39636 SRR1972985 SRX993117 SRS907736 SRP057116 PRJNA280983 Danio rerio strain:CG2 Transcriptome or Gene expression PRJNA280983 Other CG2 homozygous diploid zebrafish line.       Model organism or animal sample from Danio rerio CG2 CG2 immune related tissues   strain:CG2|dev stage:adult|sex:not determined|tissue:kidney intestine gills and spleen|BioSampleModel:Model organism or animal                 CG2 RNA seq pooled kidney intestine gills and spleen CG2 not normalized 1 A single adult CG2 zebrafish was euthanized and the kidney intestine gills and spleen were dissected and combined for RNA extraction Trizol Life Technologies. RNA was prepared for sequencing with the TruSeq RNA kit Illumina and sequenced 2 x 100 bp paired end reads on a single lane of a HiSeq2000 Illumina. Average insert size of 280 bps.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP057116     130508_I1089_FCC1VKUACXX_L2_NCSU-GSL-0100_2.fq.gz 130508_I1089_FCC1VKUACXX_L2_NCSU-GSL-0100_1.fq.gz fastq fastq 43788950600.0 218944753.0 CG2 non normalized 0:100 1:100 A:11515770713;C:10371712470;G:10317757450;T:11519383282;N:64326685 100 100     11515770713 10371712470 10317757450 11519383282 64326685 SRX993117 SRS907736 SRA258497 North Carolina State University North Carolina State University 2 0.94368 0.94427 0.05435 0.05507 0.73612 0.7376 0.53132 0.53023 100 100 B B biological fallback assumption illumina hiseq_era unknown unknown trueseq bulk unknown unknown   United States 2015-08-05 Adult Adult Multi-tissue Multi-system
39824 39824 SRR2168748 SRX1153634 SRS1036568 SRP062468 PRJNA293022 Danio rerio heart chamber specific transcriptome PRJNA293022 Whole Genome Sequencing Chamber specific transcriptome of zebrafish namely atrium ventricle and bulbus arteriosus         ASWT Heart chamber transcriptome   breed:ASWT|age:2 years|dev stage:Adult|sex:not applicable|tissue:Heart Chambers|BioSampleModel:Model organism or animal                 Zebrafish ASWT heart bulbus arteriosus transcriptome Zebrafish bulbus arteriosus Bulbus arteriosus 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062468     ZFBulbouse_cat_R1.fastq.gz ZFBulbouse_cat_R2.fastq.gz fastq fastq 31137941450.0 154148225.0 Zebrafish bulbus arteriosus 0:101 1:101 A:8841038901;C:6663109706;G:6831238323;T:8799856408;N:2698112 101 101     8841038901 6663109706 6831238323 8799856408 2698112 SRX1153634 SRS1036568 SRA289351 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 2 0.81876 0.77794 0.54672 0.51003 0.7162 0.72752 0.54114 0.5421 101 101 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   India 2016-03-01 Adult Adult Heart Cardiovascular System
39825 39825 SRR2168740 SRX1153633 SRS1036568 SRP062468 PRJNA293022 Danio rerio heart chamber specific transcriptome PRJNA293022 Whole Genome Sequencing Chamber specific transcriptome of zebrafish namely atrium ventricle and bulbus arteriosus         ASWT Heart chamber transcriptome   breed:ASWT|age:2 years|dev stage:Adult|sex:not applicable|tissue:Heart Chambers|BioSampleModel:Model organism or animal                 Zebrafish ASWT atrium specific transcriptome Zebrafish Atrium Atrium 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062468     ZFAtrium_GTGAAA_L006_cat_R2.fastq.gz ZFAtrium_GTGAAA_L006_cat_R1.fastq.gz fastq fastq 28208507150.0 139646075.0 Zebrafish Atrium 0:101 1:101 A:8151737615;C:5894384726;G:6027846905;T:8129189369;N:5348535 101 101     8151737615 5894384726 6027846905 8129189369 5348535 SRX1153633 SRS1036568 SRA289351 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 2 0.83701 0.79433 0.58576 0.54496 0.72486 0.73766 0.55105 0.54713 101 101 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   India 2015-09-08 Adult Adult Heart Cardiovascular System
39826 39826 SRR2168750 SRX1153632 SRS1036568 SRP062468 PRJNA293022 Danio rerio heart chamber specific transcriptome PRJNA293022 Whole Genome Sequencing Chamber specific transcriptome of zebrafish namely atrium ventricle and bulbus arteriosus         ASWT Heart chamber transcriptome   breed:ASWT|age:2 years|dev stage:Adult|sex:not applicable|tissue:Heart Chambers|BioSampleModel:Model organism or animal                 Zebrafish Ventricle chamber specific transcriptome Zebrafish Ventricle chamber specific transcriptome Ventricle 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062468     ZFVentricle_cat_R2.fastq.gz ZFVentricle_cat_R1.fastq.gz fastq fastq 30913187362.0 153035581.0 Zebrafish Ventricle chamber specific transcriptome 0:101 1:101 A:8230747947;C:7230918780;G:7381253230;T:8066864305;N:3403100 101 101     8230747947 7230918780 7381253230 8066864305 3403100 SRX1153632 SRS1036568 SRA289351 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 2 0.92213 0.91404 0.22257 0.21715 0.76761 0.77193 0.54625 0.54332 101 101 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   India 2016-03-01 Adult Adult Heart Cardiovascular 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");;