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25 rows where experiment.library_selection = "unspecified", experiment.platform = "ILLUMINA" and tissue_curation = "Multi-tissue"

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devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

tissue_curation 1

  • Multi-tissue · 25 ✖

technology 1

experiment.platform 1

  • ILLUMINA · 25 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • unspecified · 25 ✖

experiment.library_layout 1

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
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
36586 36586 SRR1562528 SRX204106 SRS373224 SRP017135 PRJNA179237 Danio rerio strain:SAT Transcriptome or Gene expression PRJNA179237 Other Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.     Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas Zebrafish trancriptome for protegenomic analysis zebrafish IOB JHU transcriptome                     Zebrafish transcriptome profiling for proteogenomic analysis JHU IOB zebrafish RNA Seq 1 SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiScanSQ <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017135         3901027000.0 41246200.0 zebrafish data1 0:50 1:50 A:1065764997;C:896043530;G:867105444;T:1071973870;N:139159 50 50     1065764997 896043530 867105444 1071973870 139159 SRX204106 SRS373224 SRA060234 Johns Hopkins University|Pandey Lab Johns Hopkins University 2 0.95204 0.94561 0.11416 0.11357 0.68235 0.68387 0.47537 0.47688 50 50 B B biological fallback assumption illumina early_illumina unknown unknown unknown bulk unknown unknown   United States 2015-07-22 Undetermined Undetermined Multi-tissue Multi-system
36587 36587 SRR1562529 SRX204106 SRS373224 SRP017135 PRJNA179237 Danio rerio strain:SAT Transcriptome or Gene expression PRJNA179237 Other Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.     Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas Zebrafish trancriptome for protegenomic analysis zebrafish IOB JHU transcriptome                     Zebrafish transcriptome profiling for proteogenomic analysis JHU IOB zebrafish RNA Seq 1 SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiScanSQ <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017135         3298508150.0 34528793.0 zebrafish data2 0:50 1:50 A:870578872;C:780299206;G:764413584;T:883098619;N:117869 50 50     870578872 780299206 764413584 883098619 117869 SRX204106 SRS373224 SRA060234 Johns Hopkins University|Pandey Lab Johns Hopkins University 2 0.96195 0.9525 0.05344 0.0528 0.77285 0.7737 0.44453 0.43789 50 50 B B biological fallback assumption illumina early_illumina unknown unknown unknown bulk unknown unknown   United States 2015-07-22 Undetermined Undetermined Multi-tissue Multi-system
36588 36588 SRR1562530 SRX204106 SRS373224 SRP017135 PRJNA179237 Danio rerio strain:SAT Transcriptome or Gene expression PRJNA179237 Other Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.     Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas Zebrafish trancriptome for protegenomic analysis zebrafish IOB JHU transcriptome                     Zebrafish transcriptome profiling for proteogenomic analysis JHU IOB zebrafish RNA Seq 1 SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiScanSQ <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017135         5033866800.0 52047991.0 zebrafish data6 0:50 1:50 A:1318991279;C:1193979085;G:1179037925;T:1341674073;N:184438 50 50     1318991279 1193979085 1179037925 1341674073 184438 SRX204106 SRS373224 SRA060234 Johns Hopkins University|Pandey Lab Johns Hopkins University 2 0.97568 0.97028 0.03448 0.03488 0.88767 0.88785 0.17745 0.18337 50 50 B B biological fallback assumption illumina early_illumina unknown unknown unknown bulk unknown unknown   United States 2015-07-22 Undetermined Undetermined Multi-tissue Multi-system
36589 36589 SRR1562531 SRX204106 SRS373224 SRP017135 PRJNA179237 Danio rerio strain:SAT Transcriptome or Gene expression PRJNA179237 Other Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.     Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas Zebrafish trancriptome for protegenomic analysis zebrafish IOB JHU transcriptome                     Zebrafish transcriptome profiling for proteogenomic analysis JHU IOB zebrafish RNA Seq 1 SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiScanSQ <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017135         4394828000.0 45714707.0 zebrafish data3 0:50 1:50 A:1146792341;C:1067826128;G:1033443384;T:1146608253;N:157894 50 50     1146792341 1067826128 1033443384 1146608253 157894 SRX204106 SRS373224 SRA060234 Johns Hopkins University|Pandey Lab Johns Hopkins University 2 0.96496 0.95999 0.03952 0.03946 0.78571 0.78518 0.51359 0.49202 50 50 B B biological fallback assumption illumina early_illumina unknown unknown unknown bulk unknown unknown   United States 2015-07-22 Undetermined Undetermined Multi-tissue Multi-system
36590 36590 SRR1562532 SRX204106 SRS373224 SRP017135 PRJNA179237 Danio rerio strain:SAT Transcriptome or Gene expression PRJNA179237 Other Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.     Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas Zebrafish trancriptome for protegenomic analysis zebrafish IOB JHU transcriptome                     Zebrafish transcriptome profiling for proteogenomic analysis JHU IOB zebrafish RNA Seq 1 SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiScanSQ <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017135         3637203400.0 38182310.0 zebrafish data4 0:50 1:50 A:956604323;C:863740756;G:843429871;T:973297634;N:130816 50 50     956604323 863740756 843429871 973297634 130816 SRX204106 SRS373224 SRA060234 Johns Hopkins University|Pandey Lab Johns Hopkins University 2 0.95377 0.94653 0.0656 0.06507 0.72448 0.72541 0.4157 0.41707 50 50 B B biological fallback assumption illumina early_illumina unknown unknown unknown bulk unknown unknown   United States 2015-07-22 Undetermined Undetermined Multi-tissue Multi-system
36591 36591 SRR1562533 SRX204106 SRS373224 SRP017135 PRJNA179237 Danio rerio strain:SAT Transcriptome or Gene expression PRJNA179237 Other Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.     Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas Zebrafish trancriptome for protegenomic analysis zebrafish IOB JHU transcriptome                     Zebrafish transcriptome profiling for proteogenomic analysis JHU IOB zebrafish RNA Seq 1 SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiScanSQ <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017135         4185424200.0 44832788.0 zebrafish data5 0:50 1:50 A:1143949920;C:959926497;G:921201865;T:1160194111;N:151807 50 50     1143949920 959926497 921201865 1160194111 151807 SRX204106 SRS373224 SRA060234 Johns Hopkins University|Pandey Lab Johns Hopkins University 2 0.95163 0.94301 0.12015 0.11974 0.64396 0.64514 0.49698 0.49883 50 50 B B biological fallback assumption illumina early_illumina unknown unknown unknown bulk unknown unknown   United States 2015-07-22 Undetermined Undetermined Multi-tissue Multi-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

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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");;