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We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.", null, null, null, "heart sample from 7 mpf zebrafish replicate5", "SAMD00152454", null, "sample name:h07 5|age:7 month|biological replicate:5|tissue:heart", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing of SAMD00152454", "DRX153125", "1", "1", "Illumina TruSeq Stranded mRNA HT Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "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>", "DRP004696", "Illumina HiSeq 2000 paired end sequencing of SAMD00152454", null, null, null, 979233200.0, 4896166.0, "DRR162506", "0:100 1:100", "A:249561707;C:239388088;G:240240872;T:248407989;N:1634544", 100, 100, null, null, 249561707, 239388088, 240240872, 248407989, 1634544, "DRX153125", "DRS083186", "DRA007711", "UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology", "Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo", 2, 0.9639, 0.93711, 0.08232, 0.07857, 0.7835, 0.79198, 0.52539, 0.51656, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-12-24", "Adult", "Adult", "Heart", "Cardiovascular System"], [236, "DRR162505", "DRX153124", "DRS083185", "DRP004696", "PRJDB7713", "Age associated transcriptome analysis in 5 tissues of zebrafish", "DRP004696", "Transcriptome Analysis", "We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.", null, null, null, "heart sample from 7 mpf zebrafish replicate4", "SAMD00152453", null, "sample name:h07 4|age:7 month|biological replicate:4|tissue:heart", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing of SAMD00152453", "DRX153124", "1", "1", "Illumina TruSeq Stranded mRNA HT Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "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>", "DRP004696", "Illumina HiSeq 2000 paired end sequencing of SAMD00152453", null, null, null, 633922400.0, 3169612.0, "DRR162505", "0:100 1:100", "A:158236352;C:158464487;G:159505789;T:156692659;N:1023113", 100, 100, null, null, 158236352, 158464487, 159505789, 156692659, 1023113, "DRX153124", "DRS083185", "DRA007711", "UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology", "Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo", 2, 0.97351, 0.94642, 0.06401, 0.06072, 0.83721, 0.84532, 0.52177, 0.5279, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-12-24", "Adult", "Adult", "Heart", "Cardiovascular System"], [237, "DRR162504", "DRX153123", "DRS083184", "DRP004696", "PRJDB7713", "Age associated transcriptome analysis in 5 tissues of zebrafish", "DRP004696", "Transcriptome Analysis", "We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.", null, null, null, "heart sample from 7 mpf zebrafish replicate3", "SAMD00152452", null, "sample name:h07 3|age:7 month|biological replicate:3|tissue:heart", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing of SAMD00152452", "DRX153123", "1", "1", "Illumina TruSeq Stranded mRNA HT Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "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>", "DRP004696", "Illumina HiSeq 2000 paired end sequencing of SAMD00152452", null, null, null, 3134971400.0, 15674857.0, "DRR162504", "0:100 1:100", "A:848586113;C:717201130;G:718012934;T:846124340;N:5046883", 100, 100, null, null, 848586113, 717201130, 718012934, 846124340, 5046883, "DRX153123", "DRS083184", "DRA007711", "UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology", "Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo", 2, 0.95766, 0.93244, 0.06284, 0.06048, 0.7767, 0.78595, 0.5246, 0.53241, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-12-24", "Adult", "Adult", "Heart", "Cardiovascular System"], [238, "DRR162503", "DRX153122", "DRS083183", "DRP004696", "PRJDB7713", "Age associated transcriptome analysis in 5 tissues of zebrafish", "DRP004696", "Transcriptome Analysis", "We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.", null, null, null, "heart sample from 7 mpf zebrafish replicate2", "SAMD00152451", null, "sample name:h07 2|age:7 month|biological replicate:2|tissue:heart", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing of SAMD00152451", "DRX153122", "1", "1", "Illumina TruSeq Stranded mRNA HT Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "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>", "DRP004696", "Illumina HiSeq 2000 paired end sequencing of SAMD00152451", null, null, null, 1128933600.0, 5644668.0, "DRR162503", "0:100 1:100", "A:298341135;C:265514569;G:266315284;T:296956092;N:1806520", 100, 100, null, null, 298341135, 265514569, 266315284, 296956092, 1806520, "DRX153122", "DRS083183", "DRA007711", "UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology", "Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo", 2, 0.96447, 0.94022, 0.07383, 0.07032, 0.79295, 0.80075, 0.5553, 0.54794, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-12-24", "Adult", "Adult", "Heart", "Cardiovascular System"], [239, "DRR162502", "DRX153121", "DRS083182", "DRP004696", "PRJDB7713", "Age associated transcriptome analysis in 5 tissues of zebrafish", "DRP004696", "Transcriptome Analysis", "We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.", null, null, null, "heart sample from 7 mpf zebrafish replicate1", "SAMD00152450", null, "sample name:h07 1|age:7 month|biological replicate:1|tissue:heart", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing of SAMD00152450", "DRX153121", "1", "1", "Illumina TruSeq Stranded mRNA HT Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "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>", "DRP004696", "Illumina HiSeq 2000 paired end sequencing of SAMD00152450", null, null, null, 1104589000.0, 5522945.0, "DRR162502", "0:100 1:100", "A:296710605;C:254979238;G:256772800;T:294385639;N:1740718", 100, 100, null, null, 296710605, 254979238, 256772800, 294385639, 1740718, "DRX153121", "DRS083182", "DRA007711", "UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology", "Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo", 2, 0.9561, 0.92652, 0.05819, 0.05627, 0.77914, 0.78729, 0.49578, 0.52012, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-12-24", "Adult", "Adult", "Heart", "Cardiovascular System"], [8065, "ERR035546", "ERX013539", "ERS017860", "ERP000447", "PRJEB2368", "Sanger zebrafish sequencing", "E-MTAB-460", "Other", null, null, null, "Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. 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 re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.", "Zebrafish adult heart", "SAMEA782570", "Wellcome Sanger Institute", "ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782570|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult heart|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:heart|sample name:E MTAB 460:Zebrafish adult heart|sex:mixed", null, null, null, null, null, null, null, null, "Sanger zebrafish sequencing", "E MTAB 460 part2:5625 2", "ZFheart 2 RNA 1523493", "Sanger zebrafish sequencing", "Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. 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 re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was enriched for polyA+ RNA by 2 rounds of polyA pull down with magnetic beads and included a DNase treatment between the 2 rounds. RNA was chemically fragmented  LiCl precipitated  reverse transcribed with random primers  a second strand synthesized and made into a standard Illumina library with a fragment size of 250 to 300 bp.", "Experimental Factor: ORGANISM PART:heart", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</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>Technical Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>2</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>85</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP000447", "Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing", "ENA FIRST PUBLIC:2011 06 14|ENA LAST UPDATE:2018 11 16", "5625_2.srf", "srf", 4268641920.0, 26679012.0, "E MTAB 460 part2:5625 2.srf", "0:76 1:8 2:76", "A:1091431814;C:927546313;G:930574449;T:1098343870;N:7313378", 76, 8, 76, null, 1091431814, 927546313, 930574449, 1098343870, 7313378, "ERX013539", "ERS017860", "ERA033503", "SC|Wellcome Trust Sanger Institute", "SC|Wellcome Trust Sanger Institute", 2, 0.89019, 0.88267, 0.09729, 0.09648, 0.75396, 0.75682, 0.49617, 0.48086, 76, 76, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2011-02-03", "Adult", "Adult", "Heart", "Cardiovascular System"], [8071, "ERR023150", "ERX009447", "ERS017860", "ERP000447", "PRJEB2368", "Sanger zebrafish sequencing", "E-MTAB-460", "Other", null, null, null, "Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. 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 re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.", "Zebrafish adult heart", "SAMEA782570", "Wellcome Sanger Institute", "ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782570|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult heart|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:heart|sample name:E MTAB 460:Zebrafish adult heart|sex:mixed", null, null, null, null, null, null, null, null, "Sanger zebrafish sequencing", "E MTAB 460:4191 7", "RNA from Zebrafish adult heart", "Sanger zebrafish sequencing", "Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. 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 re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.", "Experimental Factor: ORGANISM PART:heart", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP000447", "Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing", "ENA FIRST PUBLIC:2011 02 03|ENA LAST UPDATE:2018 11 16", "4191_7.srf", "srf", 3679011648.0, 24204024.0, "E MTAB 460:4191 7.srf", "0:76 1:76", "A:1284614952;C:552903359;G:563080702;T:1273094378;N:5318257", 76, 76, null, null, 1284614952, 552903359, 563080702, 1273094378, 5318257, "ERX009447", "ERS017860", "ERA015648", "SC|Wellcome Trust Sanger Institute", "SC|Wellcome Trust Sanger Institute", 2, 0.85359, 0.84739, 0.30719, 0.3063, 0.82806, 0.82686, 0.52003, 0.52279, 76, 76, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2011-02-03", "Adult", "Adult", "Heart", "Cardiovascular System"], [8073, "ERR023145", "ERX009445", "ERS017860", "ERP000447", "PRJEB2368", "Sanger zebrafish sequencing", "E-MTAB-460", "Other", null, null, null, "Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. 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 re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.", "Zebrafish adult heart", "SAMEA782570", "Wellcome Sanger Institute", "ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782570|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult heart|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:heart|sample name:E MTAB 460:Zebrafish adult heart|sex:mixed", null, null, null, null, null, null, null, null, "Sanger zebrafish sequencing", "E MTAB 460:3212 7", "RNA from Zebrafish adult heart", "Sanger zebrafish sequencing", "Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. 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 re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.", "Experimental Factor: ORGANISM PART:heart", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP000447", "Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing", "ENA FIRST PUBLIC:2011 02 03|ENA LAST UPDATE:2018 11 16", "3212_7.srf", "srf", 590858656.0, 3887228.0, "E MTAB 460:3212 7.srf", "0:76 1:76", "A:198026008;C:95340719;G:91816629;T:200078264;N:5597036", 76, 76, null, null, 198026008, 95340719, 91816629, 200078264, 5597036, "ERX009445", "ERS017860", "ERA015648", "SC|Wellcome Trust Sanger Institute", "SC|Wellcome Trust Sanger Institute", 2, 0.85463, 0.85526, 0.2737, 0.27538, 0.82189, 0.82282, 0.55114, 0.5482, 76, 76, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2011-02-03", "Adult", "Adult", "Heart", "Cardiovascular System"], [11174, "ERR10180601", "ERX9716167", "ERS13447543", "ERP140949", "PRJEB56027", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E-MTAB-12172", "Transcriptome Analysis", "To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", null, "Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.", "lens WT 2", "SAMEA111349996", "Vanderbilt Univiersity", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349996|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens WT 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:lens|sample name:E MTAB 12172:lens WT 2|sex:male", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E MTAB 12172:lens WT 2 p", "lens WT 2 p", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.", "Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140949", "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", "5089-PP-2-CCATCCGC-AAGGCGTA_S01_L005_R1_001.fastq.gz 5089-PP-2-CCATCCGC-AAGGCGTA_S01_L005_R2_001.fastq.gz", "fastq fastq", 16333543200.0, 54445144.0, "E MTAB 12172:5089 PP 2 CCATCCGC AAGGCGTA S01 L005 R", "0:150 1:150", "A:4190619330;C:3994540430;G:4078805527;T:4069157225;N:420688", 150, 150, null, null, 4190619330, 3994540430, 4078805527, 4069157225, 420688, "ERX9716167", "ERS13447543", "ERA17903080", "Vanderbilt Univiersity|European Nucleotide Archive", "Vanderbilt Univiersity|European Nucleotide Archive", 2, 0.93689, 0.9406, 0.04209, 0.04067, 0.82698, 0.82666, 0.36086, 0.43109, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-09-24", "Adult", "Adult", "Heart", "Cardiovascular System"], [11175, "ERR10180600", "ERX9716166", "ERS13447542", "ERP140949", "PRJEB56027", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E-MTAB-12172", "Transcriptome Analysis", "To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", null, "Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.", "lens WT 1", "SAMEA111349995", "Vanderbilt Univiersity", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349995|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens WT 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:lens|sample name:E MTAB 12172:lens WT 1|sex:male", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E MTAB 12172:lens WT 1 p", "lens WT 1 p", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.", "Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140949", "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", "5089-PP-1-ACAAGGCA-TCGCGCAA_S01_L005_R1_001.fastq.gz 5089-PP-1-ACAAGGCA-TCGCGCAA_S01_L005_R2_001.fastq.gz", "fastq fastq", 15407010900.0, 51356703.0, "E MTAB 12172:5089 PP 1 ACAAGGCA TCGCGCAA S01 L005 R", "0:150 1:150", "A:3964097798;C:3754084768;G:3842793010;T:3845637263;N:398061", 150, 150, null, null, 3964097798, 3754084768, 3842793010, 3845637263, 398061, "ERX9716166", "ERS13447542", "ERA17903080", "Vanderbilt Univiersity|European Nucleotide Archive", "Vanderbilt Univiersity|European Nucleotide Archive", 2, 0.94811, 0.95125, 0.04583, 0.044, 0.81844, 0.81836, 0.35718, 0.43545, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-09-24", "Adult", "Adult", "Heart", "Cardiovascular System"], [11176, "ERR10180599", "ERX9716165", "ERS13447541", "ERP140949", "PRJEB56027", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E-MTAB-12172", "Transcriptome Analysis", "To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", null, "Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.", "lens nrf2 mut 2", "SAMEA111349994", "Vanderbilt Univiersity", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349994|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens nrf2 mut 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:nrf2 mutant|organism part:lens|sample name:E MTAB 12172:lens nrf2 mut 2|sex:male", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E MTAB 12172:lens nrf2 mut 2 p", "lens nrf2 mut 2 p", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.", "Experimental Factor: genotype:nrf2 mutant", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140949", "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", "5089-PP-6-ACCAACAG-GTTTGCTC_S01_L005_R1_001.fastq.gz 5089-PP-6-ACCAACAG-GTTTGCTC_S01_L005_R2_001.fastq.gz", "fastq fastq", 16160592300.0, 53868641.0, "E MTAB 12172:5089 PP 6 ACCAACAG GTTTGCTC S01 L005 R", "0:150 1:150", "A:4169968181;C:3949888212;G:4033930705;T:4006382078;N:423124", 150, 150, null, null, 4169968181, 3949888212, 4033930705, 4006382078, 423124, "ERX9716165", "ERS13447541", "ERA17903080", "Vanderbilt Univiersity|European Nucleotide Archive", "Vanderbilt Univiersity|European Nucleotide Archive", 2, 0.96029, 0.95994, 0.04416, 0.04259, 0.82035, 0.81982, 0.36027, 0.36601, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-09-24", "Adult", "Adult", "Heart", "Cardiovascular System"], [11177, "ERR10180598", "ERX9716164", "ERS13447540", "ERP140949", "PRJEB56027", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E-MTAB-12172", "Transcriptome Analysis", "To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", null, "Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.", "lens nrf2 mut 1", "SAMEA111349993", "Vanderbilt Univiersity", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349993|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens nrf2 mut 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:nrf2 mutant|organism part:lens|sample name:E MTAB 12172:lens nrf2 mut 1|sex:male", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E MTAB 12172:lens nrf2 mut 1 p", "lens nrf2 mut 1 p", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.", "Experimental Factor: genotype:nrf2 mutant", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140949", "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", "5089-PP-5-GCACACAA-CTTGACGA_S01_L005_R1_001.fastq.gz 5089-PP-5-GCACACAA-CTTGACGA_S01_L005_R2_001.fastq.gz", "fastq fastq", 13265052900.0, 44216843.0, "E MTAB 12172:5089 PP 5 GCACACAA CTTGACGA S01 L005 R", "0:150 1:150", "A:3416009346;C:3243776635;G:3305220346;T:3299701557;N:345016", 150, 150, null, null, 3416009346, 3243776635, 3305220346, 3299701557, 345016, "ERX9716164", "ERS13447540", "ERA17903080", "Vanderbilt Univiersity|European Nucleotide Archive", "Vanderbilt Univiersity|European Nucleotide Archive", 2, 0.96137, 0.95958, 0.04396, 0.04235, 0.81505, 0.8156, 0.42582, 0.44063, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-09-24", "Adult", "Adult", "Heart", "Cardiovascular System"], [11178, "ERR10180597", "ERX9716163", "ERS13447539", "ERP140949", "PRJEB56027", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E-MTAB-12172", "Transcriptome Analysis", "To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", null, "Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.", "lens abanrf2 mut 2", "SAMEA111349992", "Vanderbilt Univiersity", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349992|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens abanrf2 mut 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout; nrf2 double mutant|organism part:lens|sample name:E MTAB 12172:lens abanrf2 mut 2|sex:male", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E MTAB 12172:lens abanrf2 mut 2 p", "lens abanrf2 mut 2 p", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.", "Experimental Factor: genotype:cryaba knockout; nrf2 double mutant", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140949", "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", "5089-PP-8-AACACCAC-GGTGTGAG_S01_L005_R1_001.fastq.gz 5089-PP-8-AACACCAC-GGTGTGAG_S01_L005_R2_001.fastq.gz", "fastq fastq", 15388634400.0, 51295448.0, "E MTAB 12172:5089 PP 8 AACACCAC GGTGTGAG S01 L005 R", "0:150 1:150", "A:3958631492;C:3788327811;G:3838374812;T:3802892334;N:407951", 150, 150, null, null, 3958631492, 3788327811, 3838374812, 3802892334, 407951, "ERX9716163", "ERS13447539", "ERA17903080", "Vanderbilt Univiersity|European Nucleotide Archive", "Vanderbilt Univiersity|European Nucleotide Archive", 2, 0.95795, 0.95848, 0.03631, 0.0352, 0.82686, 0.82702, 0.44398, 0.43981, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-09-24", "Adult", "Adult", "Heart", "Cardiovascular System"], [11179, "ERR10180596", "ERX9716162", "ERS13447538", "ERP140949", "PRJEB56027", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E-MTAB-12172", "Transcriptome Analysis", "To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", null, "Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.", "lens abanrf2 mut 1", "SAMEA111349991", "Vanderbilt Univiersity", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349991|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens abanrf2 mut 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout; nrf2 double mutant|organism part:lens|sample name:E MTAB 12172:lens abanrf2 mut 1|sex:male", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E MTAB 12172:lens abanrf2 mut 1 p", "lens abanrf2 mut 1 p", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.", "Experimental Factor: genotype:cryaba knockout; nrf2 double mutant", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140949", "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", "5089-PP-7-ATGTTCCT-TCAGCGCC_S01_L005_R1_001.fastq.gz 5089-PP-7-ATGTTCCT-TCAGCGCC_S01_L005_R2_001.fastq.gz", "fastq fastq", 15994173600.0, 53313912.0, "E MTAB 12172:5089 PP 7 ATGTTCCT TCAGCGCC S01 L005 R", "0:150 1:150", "A:4099988245;C:3917478063;G:3992545834;T:3983743906;N:417552", 150, 150, null, null, 4099988245, 3917478063, 3992545834, 3983743906, 417552, "ERX9716162", "ERS13447538", "ERA17903080", "Vanderbilt Univiersity|European Nucleotide Archive", "Vanderbilt Univiersity|European Nucleotide Archive", 2, 0.96127, 0.95941, 0.04117, 0.03964, 0.82047, 0.82057, 0.38606, 0.37713, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-09-24", "Adult", "Adult", "Heart", "Cardiovascular System"], [11180, "ERR10180595", "ERX9716161", "ERS13447537", "ERP140949", "PRJEB56027", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E-MTAB-12172", "Transcriptome Analysis", "To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", null, "Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.", "lens abaKO 2", "SAMEA111349990", "Vanderbilt Univiersity", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349990|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens abaKO 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout|organism part:lens|sample name:E MTAB 12172:lens abaKO 2|sex:male", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E MTAB 12172:lens abaKO 2 p", "lens abaKO 2 p", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.", "Experimental Factor: genotype:cryaba knockout", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140949", "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", "5089-PP-4-TCGCGCAA-ACAAGGCA_S01_L005_R1_001.fastq.gz 5089-PP-4-TCGCGCAA-ACAAGGCA_S01_L005_R2_001.fastq.gz", "fastq fastq", 17799042900.0, 59330143.0, "E MTAB 12172:5089 PP 4 TCGCGCAA ACAAGGCA S01 L005 R", "0:150 1:150", "A:4545266681;C:4379648812;G:4457651334;T:4416025472;N:450601", 150, 150, null, null, 4545266681, 4379648812, 4457651334, 4416025472, 450601, "ERX9716161", "ERS13447537", "ERA17903080", "Vanderbilt Univiersity|European Nucleotide Archive", "Vanderbilt Univiersity|European Nucleotide Archive", 2, 0.8747, 0.87804, 0.03407, 0.03304, 0.83999, 0.84047, 0.41026, 0.42746, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-09-24", "Adult", "Adult", "Heart", "Cardiovascular System"], [11181, "ERR10180594", "ERX9716160", "ERS13447536", "ERP140949", "PRJEB56027", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E-MTAB-12172", "Transcriptome Analysis", "To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", null, "Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.", "lens abaKO 1", "SAMEA111349989", "Vanderbilt Univiersity", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349989|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens abaKO 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout|organism part:lens|sample name:E MTAB 12172:lens abaKO 1|sex:male", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E MTAB 12172:lens abaKO 1 p", "lens abaKO 1 p", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.", "Experimental Factor: genotype:cryaba knockout", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140949", "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", "5089-PP-3-AAGGCGTA-CCATCCGC_S01_L005_R1_001.fastq.gz 5089-PP-3-AAGGCGTA-CCATCCGC_S01_L005_R2_001.fastq.gz", "fastq fastq", 18850381500.0, 62834605.0, "E MTAB 12172:5089 PP 3 AAGGCGTA CCATCCGC S01 L005 R", "0:150 1:150", "A:4831021904;C:4613611754;G:4712103573;T:4693153324;N:490945", 150, 150, null, null, 4831021904, 4613611754, 4712103573, 4693153324, 490945, "ERX9716160", "ERS13447536", "ERA17903080", "Vanderbilt Univiersity|European Nucleotide Archive", "Vanderbilt Univiersity|European Nucleotide Archive", 2, 0.94079, 0.94389, 0.04169, 0.04008, 0.82367, 0.82524, 0.4379, 0.43771, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-09-24", "Adult", "Adult", "Heart", "Cardiovascular System"], [11182, "ERR10180593", "ERX9716159", "ERS13447535", "ERP140949", "PRJEB56027", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E-MTAB-12172", "Transcriptome Analysis", "To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", null, "Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.", "heart WT 2", "SAMEA111349988", "Vanderbilt Univiersity", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349988|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart WT 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:heart|sample name:E MTAB 12172:heart WT 2|sex:male", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E MTAB 12172:heart WT 2 p", "heart WT 2 p", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.", "Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140949", "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", "5539-JP-2-GATATGAA-TACGGCAG_S1_L001_R1_001.fastq.gz 5539-JP-2-GATATGAA-TACGGCAG_S1_L001_R2_001.fastq.gz", "fastq fastq", 14304623100.0, 47682077.0, "E MTAB 12172:5539 JP 2 GATATGAA TACGGCAG S1 L001 R", "0:150 1:150", "A:3881337642;C:3260590900;G:3395614407;T:3766879544;N:200607", 150, 150, null, null, 3881337642, 3260590900, 3395614407, 3766879544, 200607, "ERX9716159", "ERS13447535", "ERA17903080", "Vanderbilt Univiersity|European Nucleotide Archive", "Vanderbilt Univiersity|European Nucleotide Archive", 2, 0.94254, 0.94698, 0.05301, 0.05137, 0.77502, 0.77352, 0.50073, 0.50274, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-09-24", "Adult", "Adult", "Heart", "Cardiovascular System"], [11183, "ERR10180592", "ERX9716158", "ERS13447534", "ERP140949", "PRJEB56027", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E-MTAB-12172", "Transcriptome Analysis", "To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", null, "Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.", "heart WT 1", "SAMEA111349987", "Vanderbilt Univiersity", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349987|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart WT 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:heart|sample name:E MTAB 12172:heart WT 1|sex:male", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E MTAB 12172:heart WT 1 p", "heart WT 1 p", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.", "Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140949", "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", "5539-JP-1-GTCCGATC-GCCAATCC_S1_L001_R1_001.fastq.gz 5539-JP-1-GTCCGATC-GCCAATCC_S1_L001_R2_001.fastq.gz", "fastq fastq", 19185453300.0, 63951511.0, "E MTAB 12172:5539 JP 1 GTCCGATC GCCAATCC S1 L001 R", "0:150 1:150", "A:5172411335;C:4401564793;G:4571457514;T:5039775881;N:243777", 150, 150, null, null, 5172411335, 4401564793, 4571457514, 5039775881, 243777, "ERX9716158", "ERS13447534", "ERA17903080", "Vanderbilt Univiersity|European Nucleotide Archive", "Vanderbilt Univiersity|European Nucleotide Archive", 2, 0.94765, 0.95188, 0.0548, 0.05291, 0.75986, 0.76015, 0.49801, 0.49914, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-09-24", "Adult", "Adult", "Heart", "Cardiovascular System"], [11184, "ERR10180591", "ERX9716157", "ERS13447533", "ERP140949", "PRJEB56027", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E-MTAB-12172", "Transcriptome Analysis", "To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", null, "Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.", "heart nrf2 mut 2", "SAMEA111349986", "Vanderbilt Univiersity", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349986|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart nrf2 mut 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:nrf2 mutant|organism part:heart|sample name:E MTAB 12172:heart nrf2 mut 2|sex:male", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E MTAB 12172:heart nrf2 mut 2 p", "heart nrf2 mut 2 p", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.", "Experimental Factor: genotype:nrf2 mutant", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140949", "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", "5539-JP-6-CCTTTCAC-TCTTGTTT_S1_L001_R1_001.fastq.gz 5539-JP-6-CCTTTCAC-TCTTGTTT_S1_L001_R2_001.fastq.gz", "fastq fastq", 15506772300.0, 51689241.0, "E MTAB 12172:5539 JP 6 CCTTTCAC TCTTGTTT S1 L001 R", "0:150 1:150", "A:4206068868;C:3553449100;G:3659363790;T:4087684595;N:205947", 150, 150, null, null, 4206068868, 3553449100, 3659363790, 4087684595, 205947, "ERX9716157", "ERS13447533", "ERA17903080", "Vanderbilt Univiersity|European Nucleotide Archive", "Vanderbilt Univiersity|European Nucleotide Archive", 2, 0.94875, 0.95145, 0.05898, 0.05611, 0.77254, 0.77293, 0.43478, 0.41873, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-09-24", "Adult", "Adult", "Heart", "Cardiovascular System"], [11185, "ERR10180590", "ERX9716156", "ERS13447532", "ERP140949", "PRJEB56027", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E-MTAB-12172", "Transcriptome Analysis", "To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", null, "Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.", "heart nrf2 mut 1", "SAMEA111349985", "Vanderbilt Univiersity", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349985|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart nrf2 mut 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:nrf2 mutant|organism part:heart|sample name:E MTAB 12172:heart nrf2 mut 1|sex:male", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E MTAB 12172:heart nrf2 mut 1 p", "heart nrf2 mut 1 p", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.", "Experimental Factor: genotype:nrf2 mutant", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140949", "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", "5539-JP-5-CACTAGAC-TGAGGACT_S1_L001_R1_001.fastq.gz 5539-JP-5-CACTAGAC-TGAGGACT_S1_L001_R2_001.fastq.gz", "fastq fastq", 21738824700.0, 72462749.0, "E MTAB 12172:5539 JP 5 CACTAGAC TGAGGACT S1 L001 R", "0:150 1:150", "A:5871744282;C:5014617409;G:5151654454;T:5700519276;N:289279", 150, 150, null, null, 5871744282, 5014617409, 5151654454, 5700519276, 289279, "ERX9716156", "ERS13447532", "ERA17903080", "Vanderbilt Univiersity|European Nucleotide Archive", "Vanderbilt Univiersity|European Nucleotide Archive", 2, 0.95074, 0.95283, 0.05595, 0.05426, 0.77193, 0.77163, 0.43329, 0.49376, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-09-24", "Adult", "Adult", "Heart", "Cardiovascular System"], [11186, "ERR10180589", "ERX9716155", "ERS13447531", "ERP140949", "PRJEB56027", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E-MTAB-12172", "Transcriptome Analysis", "To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", null, "Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.", "heart abanrf2 mut 2", "SAMEA111349984", "Vanderbilt Univiersity", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349984|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart abanrf2 mut 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout; nrf2 double mutant|organism part:heart|sample name:E MTAB 12172:heart abanrf2 mut 2|sex:male", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E MTAB 12172:heart abanrf2 mut 2 p", "heart abanrf2 mut 2 p", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.", "Experimental Factor: genotype:cryaba knockout; nrf2 double mutant", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140949", "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", "5539-JP-8-TACGGCAG-GATATGAA_S1_L001_R1_001.fastq.gz 5539-JP-8-TACGGCAG-GATATGAA_S1_L001_R2_001.fastq.gz", "fastq fastq", 17223550800.0, 57411836.0, "E MTAB 12172:5539 JP 8 TACGGCAG GATATGAA S1 L001 R", "0:150 1:150", "A:4719158105;C:3846804288;G:4048574589;T:4608706331;N:307487", 150, 150, null, null, 4719158105, 3846804288, 4048574589, 4608706331, 307487, "ERX9716155", "ERS13447531", "ERA17903080", "Vanderbilt Univiersity|European Nucleotide Archive", "Vanderbilt Univiersity|European Nucleotide Archive", 2, 0.93762, 0.93789, 0.0641, 0.05916, 0.77171, 0.77465, 0.50708, 0.52073, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-09-24", "Adult", "Adult", "Heart", "Cardiovascular System"], [11187, "ERR10180588", "ERX9716154", "ERS13447530", "ERP140949", "PRJEB56027", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E-MTAB-12172", "Transcriptome Analysis", "To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", null, "Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.", "heart abanrf2 mut 1", "SAMEA111349983", "Vanderbilt Univiersity", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349983|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart abanrf2 mut 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout; nrf2 double mutant|organism part:heart|sample name:E MTAB 12172:heart abanrf2 mut 1|sex:male", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E MTAB 12172:heart abanrf2 mut 1 p", "heart abanrf2 mut 1 p", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.", "Experimental Factor: genotype:cryaba knockout; nrf2 double mutant", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140949", "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", "5539-JP-7-GCCAATCC-GTCCGATC_S1_L001_R1_001.fastq.gz 5539-JP-7-GCCAATCC-GTCCGATC_S1_L001_R2_001.fastq.gz", "fastq fastq", 14585545800.0, 48618486.0, "E MTAB 12172:5539 JP 7 GCCAATCC GTCCGATC S1 L001 R", "0:150 1:150", "A:3991503126;C:3300292702;G:3398962745;T:3894599059;N:188168", 150, 150, null, null, 3991503126, 3300292702, 3398962745, 3894599059, 188168, "ERX9716154", "ERS13447530", "ERA17903080", "Vanderbilt Univiersity|European Nucleotide Archive", "Vanderbilt Univiersity|European Nucleotide Archive", 2, 0.9375, 0.94022, 0.06736, 0.06462, 0.76445, 0.76495, 0.50218, 0.51223, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-09-24", "Adult", "Adult", "Heart", "Cardiovascular System"], [11188, "ERR10180587", "ERX9716153", "ERS13447529", "ERP140949", "PRJEB56027", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E-MTAB-12172", "Transcriptome Analysis", "To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", null, "Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.", "heart abaKO 2", "SAMEA111349982", "Vanderbilt Univiersity", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349982|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart abaKO 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout|organism part:heart|sample name:E MTAB 12172:heart abaKO 2|sex:male", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E MTAB 12172:heart abaKO 2 p", "heart abaKO 2 p", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.", "Experimental Factor: genotype:cryaba knockout", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140949", "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", "5539-JP-4-TGTGTCAG-CACCTGTA_S1_L001_R1_001.fastq.gz 5539-JP-4-TGTGTCAG-CACCTGTA_S1_L001_R2_001.fastq.gz", "fastq fastq", 16499634000.0, 54998780.0, "E MTAB 12172:5539 JP 4 TGTGTCAG CACCTGTA S1 L001 R", "0:150 1:150", "A:4448248023;C:3776948921;G:3924285767;T:4349924059;N:227230", 150, 150, null, null, 4448248023, 3776948921, 3924285767, 4349924059, 227230, "ERX9716153", "ERS13447529", "ERA17903080", "Vanderbilt Univiersity|European Nucleotide Archive", "Vanderbilt Univiersity|European Nucleotide Archive", 2, 0.92566, 0.92887, 0.05292, 0.05145, 0.76741, 0.76759, 0.44001, 0.44327, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-09-24", "Adult", "Adult", "Heart", "Cardiovascular System"], [11189, "ERR10180586", "ERX9716152", "ERS13447528", "ERP140949", "PRJEB56027", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E-MTAB-12172", "Transcriptome Analysis", "To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", null, "Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.", "heart abaKO 1", "SAMEA111349981", "Vanderbilt Univiersity", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349981|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart abaKO 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout|organism part:heart|sample name:E MTAB 12172:heart abaKO 1|sex:male", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "E MTAB 12172:heart abaKO 1 p", "heart abaKO 1 p", "Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cry\uf061ba / ; cryabbvu613 cry\uf061bb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.", "Experimental Factor: genotype:cryaba knockout", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140949", "Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress", "ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24", "5539-JP-3-AGTCAGGT-GTAACCAC_S1_L001_R1_001.fastq.gz 5539-JP-3-AGTCAGGT-GTAACCAC_S1_L001_R2_001.fastq.gz", "fastq fastq", 23723109000.0, 79077030.0, "E MTAB 12172:5539 JP 3 AGTCAGGT GTAACCAC S1 L001 R", "0:150 1:150", "A:6432327752;C:5406026214;G:5617874748;T:6266589522;N:290764", 150, 150, null, null, 6432327752, 5406026214, 5617874748, 6266589522, 290764, "ERX9716152", "ERS13447528", "ERA17903080", "Vanderbilt Univiersity|European Nucleotide Archive", "Vanderbilt Univiersity|European Nucleotide Archive", 2, 0.94728, 0.95029, 0.05332, 0.05201, 0.76646, 0.76838, 0.50604, 0.50579, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-09-24", "Adult", "Adult", "Heart", "Cardiovascular System"], [25170, "SRR25661605", "SRX21387413", "SRS18627977", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 FLD+/? 20 hpf CMs rep3", "GSM7714404", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 FLD+/? 20 hpf CMs rep3", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS", "GSM7714404", "GSM7714404: hand2 FLD+/? 20 hpf CMs rep3; Danio rerio; RNA Seq", "GSM7714404 r1", "GSM7714404", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_WT_het_3_R1.fastq.gz", "fastq", 2441736984.0, 34141777.0, "GSM7714404 r1", "0:71.52", "A:706186414;C:496261994;G:526176364;T:713112212;N:0", 71, null, null, null, 706186414, 496261994, 526176364, 713112212, 0, "SRX21387413", "SRS18627977", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.9026, null, 0.15816, null, 0.76278, null, 0.44042, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25171, "SRR25661606", "SRX21387412", "SRS18627976", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 FLD+/? 20 hpf CMs rep2", "GSM7714403", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 FLD+/? 20 hpf CMs rep2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS", "GSM7714403", "GSM7714403: hand2 FLD+/? 20 hpf CMs rep2; Danio rerio; RNA Seq", "GSM7714403 r1", "GSM7714403", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_WT_het_2_R1.fastq.gz", "fastq", 2185611269.0, 30558084.0, "GSM7714403 r1", "0:71.52", "A:612617675;C:458632518;G:474458738;T:639902338;N:0", 71, null, null, null, 612617675, 458632518, 474458738, 639902338, 0, "SRX21387412", "SRS18627976", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90042, null, 0.14005, null, 0.75424, null, 0.44277, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25172, "SRR25661607", "SRX21387411", "SRS18627975", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 FLD+/? 20 hpf CMs rep1", "GSM7714402", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 FLD+/? 20 hpf CMs rep1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. 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Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "WT 20 hpf CMs rep3", "GSM7714401", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "WT 20 hpf CMs rep3", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS", "GSM7714401", "GSM7714401: WT 20 hpf CMs rep3; Danio rerio; RNA Seq", "GSM7714401 r1", "GSM7714401", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_WT_CMs_3_R1.fastq.gz", "fastq", 2268251602.0, 31717610.0, "GSM7714401 r1", "0:71.51", "A:637196241;C:477782543;G:497683941;T:655588877;N:0", 71, null, null, null, 637196241, 477782543, 497683941, 655588877, 0, "SRX21387410", "SRS18627974", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90026, null, 0.13291, null, 0.78707, null, 0.40811, null, 71, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25174, "SRR25661609", "SRX21387409", "SRS18627973", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "WT 20 hpf CMs rep2", "GSM7714400", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "WT 20 hpf CMs rep2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS", "GSM7714400", "GSM7714400: WT 20 hpf CMs rep2; Danio rerio; RNA Seq", "GSM7714400 r1", "GSM7714400", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_WT_CMs_2_R1.fastq.gz", "fastq", 2195524610.0, 30700033.0, "GSM7714400 r1", "0:71.52", "A:615401741;C:462686936;G:481135567;T:636300366;N:0", 71, null, null, null, 615401741, 462686936, 481135567, 636300366, 0, "SRX21387409", "SRS18627973", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90323, null, 0.1476, null, 0.78744, null, 0.41728, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25175, "SRR25661610", "SRX21387408", "SRS18627972", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "WT 20 hpf CMs rep1", "GSM7714399", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "WT 20 hpf CMs rep1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS", "GSM7714399", "GSM7714399: WT 20 hpf CMs rep1; Danio rerio; RNA Seq", "GSM7714399 r1", "GSM7714399", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_WT_CMs_1_R1.fastq.gz", "fastq", 2258160684.0, 31576661.0, "GSM7714399 r1", "0:71.51", "A:641254288;C:471580136;G:491501482;T:653824778;N:0", 71, null, null, null, 641254288, 471580136, 491501482, 653824778, 0, "SRX21387408", "SRS18627972", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.9, null, 0.13993, null, 0.78445, null, 0.40575, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25176, "SRR25661611", "SRX21387407", "SRS18627971", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 OE 20 hpf CMs rep3", "GSM7714398", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 OE 20 hpf CMs rep3", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS", "GSM7714398", "GSM7714398: hand2 OE 20 hpf CMs rep3; Danio rerio; RNA Seq", "GSM7714398 r1", "GSM7714398", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_OE_CMs_3_R1.fastq.gz", "fastq", 1886569909.0, 26380170.0, "GSM7714398 r1", "0:71.51", "A:534874421;C:392168718;G:411533838;T:547992932;N:0", 71, null, null, null, 534874421, 392168718, 411533838, 547992932, 0, "SRX21387407", "SRS18627971", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.89968, null, 0.14763, null, 0.77881, null, 0.42601, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25177, "SRR25661612", "SRX21387406", "SRS18627970", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 OE 20 hpf CMs rep2", "GSM7714397", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 OE 20 hpf CMs rep2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS", "GSM7714397", "GSM7714397: hand2 OE 20 hpf CMs rep2; Danio rerio; RNA Seq", "GSM7714397 r1", "GSM7714397", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_OE_CMs_2_R1.fastq.gz", "fastq", 2197151812.0, 30722639.0, "GSM7714397 r1", "0:71.52", "A:617116635;C:461951919;G:481371246;T:636712012;N:0", 71, null, null, null, 617116635, 461951919, 481371246, 636712012, 0, "SRX21387406", "SRS18627970", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90877, null, 0.14744, null, 0.77191, null, 0.42845, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25178, "SRR25661613", "SRX21387405", "SRS18627969", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 OE 20 hpf CMs rep1", "GSM7714396", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 OE 20 hpf CMs rep1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS", "GSM7714396", "GSM7714396: hand2 OE 20 hpf CMs rep1; Danio rerio; RNA Seq", "GSM7714396 r1", "GSM7714396", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_OE_CMs_1_R1.fastq.gz", "fastq", 1773398936.0, 24797998.0, "GSM7714396 r1", "0:71.51", "A:495618212;C:375438077;G:390377060;T:511965587;N:0", 71, null, null, null, 495618212, 375438077, 390377060, 511965587, 0, "SRX21387405", "SRS18627969", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90769, null, 0.1387, null, 0.7768, null, 0.42096, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25179, "SRR25661614", "SRX21387404", "SRS18627968", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 FLD /  20 hpf CMs rep3", "GSM7714395", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 FLD /  20 hpf CMs rep3", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS", "GSM7714395", "GSM7714395: hand2 FLD /  20 hpf CMs rep3; Danio rerio; RNA Seq", "GSM7714395 r1", "GSM7714395", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_Mut_3_R1.fastq.gz", "fastq", 2179400259.0, 30471965.0, "GSM7714395 r1", "0:71.52", "A:600555691;C:468535203;G:483122661;T:627186704;N:0", 71, null, null, null, 600555691, 468535203, 483122661, 627186704, 0, "SRX21387404", "SRS18627968", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.91581, null, 0.12256, null, 0.75209, null, 0.43413, null, 71, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25180, "SRR25661615", "SRX21387403", "SRS18627967", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 FLD /  20 hpf CMs rep2", "GSM7714394", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 FLD /  20 hpf CMs rep2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS", "GSM7714394", "GSM7714394: hand2 FLD /  20 hpf CMs rep2; Danio rerio; RNA Seq", "GSM7714394 r1", "GSM7714394", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_Mut_2_R1.fastq.gz", "fastq", 2340991168.0, 32733068.0, "GSM7714394 r1", "0:71.52", "A:647423337;C:500120073;G:514803152;T:678644606;N:0", 71, null, null, null, 647423337, 500120073, 514803152, 678644606, 0, "SRX21387403", "SRS18627967", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.91231, null, 0.12561, null, 0.75118, null, 0.44445, null, 71, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25181, "SRR25661616", "SRX21387402", "SRS18627966", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 FLD /  20 hpf CMs rep1", "GSM7714393", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 FLD /  20 hpf CMs rep1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS", "GSM7714393", "GSM7714393: hand2 FLD /  20 hpf CMs rep1; Danio rerio; RNA Seq", "GSM7714393 r1", "GSM7714393", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_Mut_1_R1.fastq.gz", "fastq", 2727863036.0, 38140997.0, "GSM7714393 r1", "0:71.52", "A:760867462;C:577539041;G:596986102;T:792470431;N:0", 71, null, null, null, 760867462, 577539041, 596986102, 792470431, 0, "SRX21387402", "SRS18627966", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.91175, null, 0.1342, null, 0.75282, null, 0.44063, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [29086, "SRR27015250", "SRX22707800", "SRS19700101", "SRP475323", "PRJNA1047551", "Identification of genes important during atrial myocardial morphogenesis", "GSE249149", "Transcriptome Analysis", "Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures.  We aimed to identify the genes involved during this process  and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.", null, "pubmed:39289341", null, "Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 3", "GSM7927521", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf loc name:missing|collection date:missing", "Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 3", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf", "GSM7927521", "GSM7927521: Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 3; Danio rerio; RNA Seq", "GSM7927521 r1", "GSM7927521", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP475323", null, "loader:fastq load.py", "dst226_zbrf_clt___ACrdmct-age___72h_b03_t01_m01_R1.fastq.gz", "fastq", 1709509823.0, 28403358.0, "GSM7927521 r1", "0:60.19", "A:400293032;C:330429588;G:326652799;T:383291002;N:268843402", 60, null, null, null, 400293032, 330429588, 326652799, 383291002, 268843402, "SRX22707800", "SRS19700101", "SRA1761360", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90079, null, 0.0827, null, 0.81406, null, 0.64557, null, 35, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-12-01", "Larval", "Larval", "Heart", "Cardiovascular System"], [29087, "SRR27015251", "SRX22707799", "SRS19700100", "SRP475323", "PRJNA1047551", "Identification of genes important during atrial myocardial morphogenesis", "GSE249149", "Transcriptome Analysis", "Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures.  We aimed to identify the genes involved during this process  and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.", null, "pubmed:39289341", null, "Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 2", "GSM7927520", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf loc name:missing|collection date:missing", "Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf", "GSM7927520", "GSM7927520: Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 2; Danio rerio; RNA Seq", "GSM7927520 r1", "GSM7927520", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP475323", null, "loader:fastq load.py", "dst226_zbrf_clt___ACrdmct-age___72h_b02_t01_m01_R1.fastq.gz", "fastq", 1740891025.0, 28211981.0, "GSM7927520 r1", "0:61.71", "A:419094150;C:347792831;G:345450108;T:407537501;N:221016435", 61, null, null, null, 419094150, 347792831, 345450108, 407537501, 221016435, "SRX22707799", "SRS19700100", "SRA1761360", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90091, null, 0.13293, null, 0.78464, null, 0.54281, null, 69, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-12-01", "Larval", "Larval", "Heart", "Cardiovascular System"], [29088, "SRR27015252", "SRX22707798", "SRS19700099", "SRP475323", "PRJNA1047551", "Identification of genes important during atrial myocardial morphogenesis", "GSE249149", "Transcriptome Analysis", "Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures.  We aimed to identify the genes involved during this process  and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.", null, "pubmed:39289341", null, "Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 1", "GSM7927519", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf loc name:missing|collection date:missing", "Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf", "GSM7927519", "GSM7927519: Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 1; Danio rerio; RNA Seq", "GSM7927519 r1", "GSM7927519", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP475323", null, "loader:fastq load.py", "dst226_zbrf_clt___ACrdmct-age___72h_b01_t01_m01_R1.fastq.gz", "fastq", 1930552948.0, 30996774.0, "GSM7927519 r1", "0:62.28", "A:468769814;C:389869994;G:387622687;T:454801262;N:229489191", 62, null, null, null, 468769814, 389869994, 387622687, 454801262, 229489191, "SRX22707798", "SRS19700099", "SRA1761360", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90465, null, 0.10656, null, 0.79586, null, 0.55674, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-12-01", "Larval", "Larval", "Heart", "Cardiovascular System"], [29089, "SRR27015253", "SRX22707797", "SRS19700098", "SRP475323", "PRJNA1047551", "Identification of genes important during atrial myocardial morphogenesis", "GSE249149", "Transcriptome Analysis", "Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures.  We aimed to identify the genes involved during this process  and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.", null, "pubmed:39289341", null, "Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 3", "GSM7927518", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf loc name:missing|collection date:missing", "Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 3", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf", "GSM7927518", "GSM7927518: Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 3; Danio rerio; RNA Seq", "GSM7927518 r1", "GSM7927518", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP475323", null, "loader:fastq load.py", "dst226_zbrf_clt___ACrdmct-age___48h_b03_t01_m01_R1.fastq.gz", "fastq", 2161847345.0, 35921817.0, "GSM7927518 r1", "0:60.18", "A:505467877;C:418329045;G:416403136;T:483063599;N:338583688", 60, null, null, null, 505467877, 418329045, 416403136, 483063599, 338583688, "SRX22707797", "SRS19700098", "SRA1761360", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.89532, null, 0.08355, null, 0.82012, null, 0.68413, null, 35, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-12-01", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [29090, "SRR27015254", "SRX22707796", "SRS19700097", "SRP475323", "PRJNA1047551", "Identification of genes important during atrial myocardial morphogenesis", "GSE249149", "Transcriptome Analysis", "Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures.  We aimed to identify the genes involved during this process  and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.", null, "pubmed:39289341", null, "Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 2", "GSM7927517", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf loc name:missing|collection date:missing", "Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf", "GSM7927517", "GSM7927517: Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 2; Danio rerio; RNA Seq", "GSM7927517 r1", "GSM7927517", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP475323", null, "loader:fastq load.py", "dst226_zbrf_clt___ACrdmct-age___48h_b02_t01_m01_R1.fastq.gz", "fastq", 2065547064.0, 31863833.0, "GSM7927517 r1", "0:64.82", "A:530497695;C:434164388;G:434118538;T:518043928;N:148722515", 64, null, null, null, 530497695, 434164388, 434118538, 518043928, 148722515, "SRX22707796", "SRS19700097", "SRA1761360", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.91772, null, 0.17863, null, 0.76828, null, 0.49567, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-12-01", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [29091, "SRR27015255", "SRX22707795", "SRS19700096", "SRP475323", "PRJNA1047551", "Identification of genes important during atrial myocardial morphogenesis", "GSE249149", "Transcriptome Analysis", "Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures.  We aimed to identify the genes involved during this process  and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.", null, "pubmed:39289341", null, "Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 1", "GSM7927516", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf loc name:missing|collection date:missing", "Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf", "GSM7927516", "GSM7927516: Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 1; Danio rerio; RNA Seq", "GSM7927516 r1", "GSM7927516", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP475323", null, "loader:fastq load.py", "dst226_zbrf_clt___ACrdmct-age___48h_b01_t01_m01_R1.fastq.gz", "fastq", 1619268089.0, 24941754.0, "GSM7927516 r1", "0:64.92", "A:410578311;C:344485123;G:343852178;T:401558739;N:118793738", 64, null, null, null, 410578311, 344485123, 343852178, 401558739, 118793738, "SRX22707795", "SRS19700096", "SRA1761360", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.91693, null, 0.13175, null, 0.77082, null, 0.47511, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-12-01", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [29145, "SRR32025076", "SRX27375413", "SRS23810876", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "qKO 5  biol rep 1  adult aorta  3 aortas pooled", "GSM8741276", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 5  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741276", "GSM8741276: qKO 5  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741276 r1", "GSM8741276", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "10_qKO_B9_R1.fastq.gz", "fastq", 1749103950.0, 23321386.0, "GSM8741276 r1", "0:75", "A:608737363;C:302455983;G:338119173;T:499492171;N:299260", 75, null, null, null, 608737363, 302455983, 338119173, 499492171, 299260, "SRX27375413", "SRS23810876", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29146, "SRR32025077", "SRX27375412", "SRS23810877", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "qKO 4  biol rep 1  adult aorta  3 aortas pooled", "GSM8741275", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 4  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741275", "GSM8741275: qKO 4  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741275 r1", "GSM8741275", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "9_qKO_A9_R1.fastq.gz", "fastq", 1391151150.0, 18548682.0, "GSM8741275 r1", "0:75", "A:493715157;C:235480005;G:265878909;T:395857913;N:219166", 75, null, null, null, 493715157, 235480005, 265878909, 395857913, 219166, "SRX27375412", "SRS23810877", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29147, "SRR32025078", "SRX27375411", "SRS23810875", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "qKO 3  biol rep 1  adult aorta  3 aortas pooled", "GSM8741274", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 3  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741274", "GSM8741274: qKO 3  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741274 r1", "GSM8741274", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "8_qKO_H8_R1.fastq.gz", "fastq", 1548693000.0, 20649240.0, "GSM8741274 r1", "0:75", "A:546086416;C:265907989;G:302995102;T:433434795;N:268698", 75, null, null, null, 546086416, 265907989, 302995102, 433434795, 268698, "SRX27375411", "SRS23810875", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29148, "SRR32025079", "SRX27375410", "SRS23810873", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "qKO 2  biol rep 1  adult aorta  3 aortas pooled", "GSM8741273", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 2  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741273", "GSM8741273: qKO 2  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741273 r1", "GSM8741273", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "7_qKO_G8_R1.fastq.gz", "fastq", 1420837575.0, 18944501.0, "GSM8741273 r1", "0:75", "A:505066296;C:237130175;G:277345211;T:401058536;N:237357", 75, null, null, null, 505066296, 237130175, 277345211, 401058536, 237357, "SRX27375410", "SRS23810873", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29149, "SRR32025080", "SRX27375409", "SRS23810874", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "qKO 1  biol rep 1  adult aorta  3 aortas pooled", "GSM8741272", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 1  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741272", "GSM8741272: qKO 1  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741272 r1", "GSM8741272", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "6_qKO_F8_R1.fastq.gz", "fastq", 1486031025.0, 19813747.0, "GSM8741272 r1", "0:75", "A:520876345;C:250796628;G:293184034;T:420907913;N:266105", 75, null, null, null, 520876345, 250796628, 293184034, 420907913, 266105, "SRX27375409", "SRS23810874", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29150, "SRR32025081", "SRX27375408", "SRS23810872", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "control 5  biol rep 1  adult aorta  3 aortas pooled", "GSM8741271", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 5  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741271", "GSM8741271: control 5  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741271 r1", "GSM8741271", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "5_wt_control_E8_R1.fastq.gz", "fastq", 1415975175.0, 18879669.0, "GSM8741271 r1", "0:75", "A:499498659;C:237283969;G:278581269;T:400389063;N:222215", 75, null, null, null, 499498659, 237283969, 278581269, 400389063, 222215, "SRX27375408", "SRS23810872", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29151, "SRR32025082", "SRX27375407", "SRS23810871", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "control 4  biol rep 1  adult aorta  3 aortas pooled", "GSM8741270", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 4  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741270", "GSM8741270: control 4  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741270 r1", "GSM8741270", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "4_wt_control_D8_R1.fastq.gz", "fastq", 1448565375.0, 19314205.0, "GSM8741270 r1", "0:75", "A:515361139;C:240035739;G:286658162;T:406262131;N:248204", 75, null, null, null, 515361139, 240035739, 286658162, 406262131, 248204, "SRX27375407", "SRS23810871", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29152, "SRR32025083", "SRX27375406", "SRS23810870", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "control 3  biol rep 1  adult aorta  3 aortas pooled", "GSM8741269", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 3  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741269", "GSM8741269: control 3  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741269 r1", "GSM8741269", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "3_wt_control_C8_R1.fastq.gz", "fastq", 1171513275.0, 15620177.0, "GSM8741269 r1", "0:75", "A:417371801;C:198042286;G:227929434;T:328006138;N:163616", 75, null, null, null, 417371801, 198042286, 227929434, 328006138, 163616, "SRX27375406", "SRS23810870", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29153, "SRR32025084", "SRX27375405", "SRS23810869", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "control 2  biol rep 1  adult aorta  3 aortas pooled", "GSM8741268", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 2  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741268", "GSM8741268: control 2  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741268 r1", "GSM8741268", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "2_wt_control_B8_R1.fastq.gz", "fastq", 1379973000.0, 18399640.0, "GSM8741268 r1", "0:75", "A:487735196;C:232122567;G:270442978;T:389464154;N:208105", 75, null, null, null, 487735196, 232122567, 270442978, 389464154, 208105, "SRX27375405", "SRS23810869", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29154, "SRR32025085", "SRX27375404", "SRS23810868", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "control 1  biol rep 1  adult aorta  3 aortas pooled", "GSM8741267", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 1  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741267", "GSM8741267: control 1  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741267 r1", "GSM8741267", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "1_wt_control_A8_R1.fastq.gz", "fastq", 1068193125.0, 14242575.0, "GSM8741267 r1", "0:75", "A:379776425;C:179521683;G:209337737;T:299415096;N:142184", 75, null, null, null, 379776425, 179521683, 209337737, 299415096, 142184, "SRX27375404", "SRS23810868", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29569, "SRR27368685", "SRX23045203", "SRS20006222", "SRP480346", "PRJNA1057908", "An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]", "GSE252151", "Transcriptome Analysis", "cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However  cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types  predominantly cardiomyocytes. Therefore  cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development  as they share a number of physiological features with the human heart during development. Therefore  we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling  providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes  validating these genomic regions as cardiac regulatory elements. We share this comprehensive  reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells  n=3 biological replicates and GFP negative cells 500 000 cells  n=3 biological replicates were collected  and RNA sequencing was performed on these samples.", "parent bioproject:PRJNA1057890", null, null, "500kGFPneg6 Non cardiomyocytes", "GSM7995233", null, "source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control|geo loc name:missing|collection date:missing", "500kGFPneg6 Non cardiomyocytes", "FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin  2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al  2018  using default parameters. There were two sets of counts obtained  the first were the reads mapped to genome Zv9  and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9  Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample", "Heart", null, "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control", "GSM7995233", "GSM7995233: 500kGFPneg6 Non cardiomyocytes; Danio rerio; RNA Seq", "GSM7995233 r1", "GSM7995233", "1", "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP480346", null, null, "500kGFPneg6_S42_L008_R1_001.fastq.gz", "fastq", 527477356.0, 10449387.0, "GSM7995233 r1", "0:50.48", "A:141759410;C:113279303;G:116384028;T:155860577;N:194038", 50, null, null, null, 141759410, 113279303, 116384028, 155860577, 194038, "SRX23045203", "SRS20006222", "SRA1776396", "Australian Regenerative Medicine Institute, Monash University", "Australian Regenerative Medicine Institute, Monash University", 1, 0.79175, null, 0.2711, null, 0.7587, null, 0.61924, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-12-27", "Undetermined", "Larval", "Heart", "Cardiovascular System"], [29570, "SRR27368686", "SRX23045202", "SRS20006221", "SRP480346", "PRJNA1057908", "An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]", "GSE252151", "Transcriptome Analysis", "cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However  cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types  predominantly cardiomyocytes. Therefore  cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development  as they share a number of physiological features with the human heart during development. Therefore  we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling  providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes  validating these genomic regions as cardiac regulatory elements. We share this comprehensive  reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells  n=3 biological replicates and GFP negative cells 500 000 cells  n=3 biological replicates were collected  and RNA sequencing was performed on these samples.", "parent bioproject:PRJNA1057890", null, null, "500kGFPneg5 Non cardiomyocytes", "GSM7995232", null, "source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control|geo loc name:missing|collection date:missing", "500kGFPneg5 Non cardiomyocytes", "FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin  2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al  2018  using default parameters. There were two sets of counts obtained  the first were the reads mapped to genome Zv9  and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9  Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample", "Heart", null, "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control", "GSM7995232", "GSM7995232: 500kGFPneg5 Non cardiomyocytes; Danio rerio; RNA Seq", "GSM7995232 r1", "GSM7995232", "1", "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP480346", null, null, "500kGFPneg5_S41_L008_R1_001.fastq.gz", "fastq", 3356204764.0, 66511806.0, "GSM7995232 r1", "0:50.46", "A:860342578;C:766593257;G:774473426;T:953992775;N:802728", 50, null, null, null, 860342578, 766593257, 774473426, 953992775, 802728, "SRX23045202", "SRS20006221", "SRA1776396", "Australian Regenerative Medicine Institute, Monash University", "Australian Regenerative Medicine Institute, Monash University", 1, 0.70469, null, 0.23332, null, 0.76992, null, 0.62712, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-12-27", "Undetermined", "Larval", "Heart", "Cardiovascular System"], [29571, "SRR27368687", "SRX23045201", "SRS20006220", "SRP480346", "PRJNA1057908", "An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]", "GSE252151", "Transcriptome Analysis", "cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However  cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types  predominantly cardiomyocytes. Therefore  cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development  as they share a number of physiological features with the human heart during development. Therefore  we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling  providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes  validating these genomic regions as cardiac regulatory elements. We share this comprehensive  reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells  n=3 biological replicates and GFP negative cells 500 000 cells  n=3 biological replicates were collected  and RNA sequencing was performed on these samples.", "parent bioproject:PRJNA1057890", null, null, "500kGFPneg4 Non cardiomyocytes", "GSM7995231", null, "source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control|geo loc name:missing|collection date:missing", "500kGFPneg4 Non cardiomyocytes", "FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin  2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al  2018  using default parameters. There were two sets of counts obtained  the first were the reads mapped to genome Zv9  and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9  Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample", "Heart", null, "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control", "GSM7995231", "GSM7995231: 500kGFPneg4 Non cardiomyocytes; Danio rerio; RNA Seq", "GSM7995231 r1", "GSM7995231", "1", "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP480346", null, null, "500kGFPneg4_S40_L008_R1_001.fastq.gz", "fastq", 3075367681.0, 60986692.0, "GSM7995231 r1", "0:50.43", "A:807059039;C:682279458;G:696326840;T:888937765;N:764579", 50, null, null, null, 807059039, 682279458, 696326840, 888937765, 764579, "SRX23045201", "SRS20006220", "SRA1776396", "Australian Regenerative Medicine Institute, Monash University", "Australian Regenerative Medicine Institute, Monash University", 1, 0.74255, null, 0.26699, null, 0.76786, null, 0.63053, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-12-27", "Undetermined", "Larval", "Heart", "Cardiovascular System"], [29572, "SRR27368688", "SRX23045200", "SRS20006219", "SRP480346", "PRJNA1057908", "An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]", "GSE252151", "Transcriptome Analysis", "cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However  cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types  predominantly cardiomyocytes. Therefore  cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development  as they share a number of physiological features with the human heart during development. Therefore  we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling  providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes  validating these genomic regions as cardiac regulatory elements. We share this comprehensive  reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells  n=3 biological replicates and GFP negative cells 500 000 cells  n=3 biological replicates were collected  and RNA sequencing was performed on these samples.", "parent bioproject:PRJNA1057890", null, null, "30kGFPpos3 Cardiomyocytes", "GSM7995230", null, "source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control|geo loc name:missing|collection date:missing", "30kGFPpos3 Cardiomyocytes", "FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin  2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al  2018  using default parameters. There were two sets of counts obtained  the first were the reads mapped to genome Zv9  and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9  Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample", "Heart", null, "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control", "GSM7995230", "GSM7995230: 30kGFPpos3 Cardiomyocytes; Danio rerio; RNA Seq", "GSM7995230 r1", "GSM7995230", "1", "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP480346", null, null, "30kGFPpos3_S39_L008_R1_001.fastq.gz", "fastq", 2938808771.0, 58361915.0, "GSM7995230 r1", "0:50.35", "A:533261626;C:883704329;G:825929620;T:694986734;N:926462", 50, null, null, null, 533261626, 883704329, 825929620, 694986734, 926462, "SRX23045200", "SRS20006219", "SRA1776396", "Australian Regenerative Medicine Institute, Monash University", "Australian Regenerative Medicine Institute, Monash University", 1, 0.12924, null, 0.05415, null, 0.92034, null, 0.70896, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-12-27", "Undetermined", "Larval", "Heart", "Cardiovascular System"], [29573, "SRR27368689", "SRX23045199", "SRS20006218", "SRP480346", "PRJNA1057908", "An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]", "GSE252151", "Transcriptome Analysis", "cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However  cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types  predominantly cardiomyocytes. Therefore  cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development  as they share a number of physiological features with the human heart during development. Therefore  we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling  providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes  validating these genomic regions as cardiac regulatory elements. We share this comprehensive  reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells  n=3 biological replicates and GFP negative cells 500 000 cells  n=3 biological replicates were collected  and RNA sequencing was performed on these samples.", "parent bioproject:PRJNA1057890", null, null, "30kGFPpos2 Cardiomyocytes", "GSM7995229", null, "source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control|geo loc name:missing|collection date:missing", "30kGFPpos2 Cardiomyocytes", "FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin  2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al  2018  using default parameters. There were two sets of counts obtained  the first were the reads mapped to genome Zv9  and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9  Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample", "Heart", null, "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control", "GSM7995229", "GSM7995229: 30kGFPpos2 Cardiomyocytes; Danio rerio; RNA Seq", "GSM7995229 r1", "GSM7995229", "1", "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP480346", null, null, "30kGFPpos2_S38_L008_R1_001.fastq.gz", "fastq", 3006409096.0, 59645543.0, "GSM7995229 r1", "0:50.40", "A:560839480;C:885691877;G:830121593;T:728932219;N:823927", 50, null, null, null, 560839480, 885691877, 830121593, 728932219, 823927, "SRX23045199", "SRS20006218", "SRA1776396", "Australian Regenerative Medicine Institute, Monash University", "Australian Regenerative Medicine Institute, Monash University", 1, 0.17805, null, 0.06115, null, 0.89769, null, 0.68731, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-12-27", "Undetermined", "Larval", "Heart", "Cardiovascular System"], [29574, "SRR27368690", "SRX23045198", "SRS20006217", "SRP480346", "PRJNA1057908", "An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]", "GSE252151", "Transcriptome Analysis", "cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However  cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types  predominantly cardiomyocytes. Therefore  cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development  as they share a number of physiological features with the human heart during development. Therefore  we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling  providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes  validating these genomic regions as cardiac regulatory elements. We share this comprehensive  reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells  n=3 biological replicates and GFP negative cells 500 000 cells  n=3 biological replicates were collected  and RNA sequencing was performed on these samples.", "parent bioproject:PRJNA1057890", null, null, "30kGFPpos1 Cardiomyocytes", "GSM7995228", null, "source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control|geo loc name:missing|collection date:missing", "30kGFPpos1 Cardiomyocytes", "FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin  2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al  2018  using default parameters. There were two sets of counts obtained  the first were the reads mapped to genome Zv9  and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9  Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample", "Heart", null, "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control", "GSM7995228", "GSM7995228: 30kGFPpos1 Cardiomyocytes; Danio rerio; RNA Seq", "GSM7995228 r1", "GSM7995228", "1", "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP480346", null, null, "30kGFPpos1_S37_L008_R1_001.fastq.gz", "fastq", 3254639839.0, 64665631.0, "GSM7995228 r1", "0:50.33", "A:545193535;C:1023804678;G:938318027;T:746302007;N:1021592", 50, null, null, null, 545193535, 1023804678, 938318027, 746302007, 1021592, "SRX23045198", "SRS20006217", "SRA1776396", "Australian Regenerative Medicine Institute, Monash University", "Australian Regenerative Medicine Institute, Monash University", 1, 0.05453, null, 0.01921, null, 0.9643, null, 0.78064, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-12-27", "Undetermined", "Larval", "Heart", "Cardiovascular System"], [30512, "SRR27764782", "SRX23429747", "SRS20284188", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  cox7a1 /   replicate 4", "GSM8042779", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  cox7a1 /   replicate 4", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury", "GSM8042779", "GSM8042779: Cardiac ventricle  cox7a1 /   replicate 4; Danio rerio; RNA Seq", "GSM8042779 r1", "GSM8042779", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "KO_10_Directional_S8_R1_001.fastq.gz", "fastq", 8619450300.0, 86194503.0, "GSM8042779 r1", "0:100", "A:2183264320;C:2042597849;G:2002385828;T:2389908983;N:1293320", 100, null, null, null, 2183264320, 2042597849, 2002385828, 2389908983, 1293320, "SRX23429747", "SRS20284188", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30513, "SRR27764783", "SRX23429746", "SRS20284187", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  cox7a1 /   replicate 3", "GSM8042778", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  cox7a1 /   replicate 3", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury", "GSM8042778", "GSM8042778: Cardiac ventricle  cox7a1 /   replicate 3; Danio rerio; RNA Seq", "GSM8042778 r1", "GSM8042778", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "KO_9_Directional_S7_R1_001.fastq.gz", "fastq", 6466746100.0, 64667461.0, "GSM8042778 r1", "0:100", "A:1708351950;C:1464168743;G:1452219209;T:1841033764;N:972434", 100, null, null, null, 1708351950, 1464168743, 1452219209, 1841033764, 972434, "SRX23429746", "SRS20284187", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30514, "SRR27764784", "SRX23429745", "SRS20284186", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  cox7a1 /   replicate 2", "GSM8042777", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  cox7a1 /   replicate 2", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury", "GSM8042777", "GSM8042777: Cardiac ventricle  cox7a1 /   replicate 2; Danio rerio; RNA Seq", "GSM8042777 r1", "GSM8042777", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "KO_8_Directional_S6_R1_001.fastq.gz", "fastq", 6766795300.0, 67667953.0, "GSM8042777 r1", "0:100", "A:1803038642;C:1540664299;G:1518741633;T:1903355305;N:995421", 100, null, null, null, 1803038642, 1540664299, 1518741633, 1903355305, 995421, "SRX23429745", "SRS20284186", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30515, "SRR27764785", "SRX23429744", "SRS20284185", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  cox7a1 /   replicate 1", "GSM8042776", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  cox7a1 /   replicate 1", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury", "GSM8042776", "GSM8042776: Cardiac ventricle  cox7a1 /   replicate 1; Danio rerio; RNA Seq", "GSM8042776 r1", "GSM8042776", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "KO_7_Directional_S5_R1_001.fastq.gz", "fastq", 5583049300.0, 55830493.0, "GSM8042776 r1", "0:100", "A:1479820662;C:1265599242;G:1251078421;T:1585727832;N:823143", 100, null, null, null, 1479820662, 1265599242, 1251078421, 1585727832, 823143, "SRX23429744", "SRS20284185", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30516, "SRR27764786", "SRX23429743", "SRS20284184", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  wt sibling  replicate 4", "GSM8042775", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  wt sibling  replicate 4", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury", "GSM8042775", "GSM8042775: Cardiac ventricle  wt sibling  replicate 4; Danio rerio; RNA Seq", "GSM8042775 r1", "GSM8042775", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "WT_5_Directional_S4_R1_001.fastq.gz", "fastq", 6851217800.0, 68512178.0, "GSM8042775 r1", "0:100", "A:1837112549;C:1539284911;G:1515596368;T:1958221274;N:1002698", 100, null, null, null, 1837112549, 1539284911, 1515596368, 1958221274, 1002698, "SRX23429743", "SRS20284184", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30517, "SRR27764787", "SRX23429742", "SRS20284183", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  wt sibling  replicate 3", "GSM8042774", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  wt sibling  replicate 3", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury", "GSM8042774", "GSM8042774: Cardiac ventricle  wt sibling  replicate 3; Danio rerio; RNA Seq", "GSM8042774 r1", "GSM8042774", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "WT_3_Directional_S3_R1_001.fastq.gz", "fastq", 7036251700.0, 70362517.0, "GSM8042774 r1", "0:100", "A:1881612688;C:1574593657;G:1570342252;T:2008668471;N:1034632", 100, null, null, null, 1881612688, 1574593657, 1570342252, 2008668471, 1034632, "SRX23429742", "SRS20284183", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30518, "SRR27764788", "SRX23429741", "SRS20284182", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  wt sibling  replicate 2", "GSM8042773", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  wt sibling  replicate 2", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury", "GSM8042773", "GSM8042773: Cardiac ventricle  wt sibling  replicate 2; Danio rerio; RNA Seq", "GSM8042773 r1", "GSM8042773", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "WT_2_Directional_S2_R1_001.fastq.gz", "fastq", 6856428200.0, 68564282.0, "GSM8042773 r1", "0:100", "A:1790369167;C:1572129686;G:1566120109;T:1926782247;N:1026991", 100, null, null, null, 1790369167, 1572129686, 1566120109, 1926782247, 1026991, "SRX23429741", "SRS20284182", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30519, "SRR27764789", "SRX23429740", "SRS20284181", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  wt sibling  replicate 1", "GSM8042772", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  wt sibling  replicate 1", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury", "GSM8042772", "GSM8042772: Cardiac ventricle  wt sibling  replicate 1; Danio rerio; RNA Seq", "GSM8042772 r1", "GSM8042772", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "WT_1_Directional_S1_R1_001.fastq.gz", "fastq", 7089416800.0, 70894168.0, "GSM8042772 r1", "0:100", "A:1855346146;C:1626812736;G:1599932420;T:2006283874;N:1041624", 100, null, null, null, 1855346146, 1626812736, 1599932420, 2006283874, 1041624, "SRX23429740", "SRS20284181", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30708, "SRR28329751", "SRX23938186", "SRS20741667", "SRP494974", "PRJNA1087264", "Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression", "GSE261479", "Transcriptome Analysis", "Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods:  Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 \u00b5M were collected for RNA seq.", null, "pubmed:40053597", null, "DAPT 3", "GSM8144970", null, "source name:hearts|tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DAPT|geo loc name:missing|collection date:missing", "DAPT 3", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix  between treatment samples and wild type samples.", "hearts", "60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 \u03bcM  to 96 hpf.", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer\u2019s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", "Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau\u2019s Buffer at 28 \u00b0C with a photoperiod of 14/10\u2009h.", "tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DAPT", "GSM8144970", "GSM8144970: DAPT 3; Danio rerio; RNA Seq", "GSM8144970 r1", "GSM8144970", "1", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494974", null, null, "DAPT_3_1.fq.gz DAPT_3_2.fq.gz", "fastq fastq", 6899234400.0, 34496172.0, "GSM8144970 r1", "0:100 1:100", "A:1864675679;C:1564709308;G:1588106892;T:1881742521;N:0", 100, 100, null, null, 1864675679, 1564709308, 1588106892, 1881742521, 0, "SRX23938186", "SRS20741667", "SRA1823438", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", 2, 0.93368, 0.93504, 0.09899, 0.09916, 0.67174, 0.67095, 0.51572, 0.5101, 100, 100, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-03-13", "Larval", "Larval", "Heart", "Cardiovascular System"], [30709, "SRR28329752", "SRX23938185", "SRS20741666", "SRP494974", "PRJNA1087264", "Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression", "GSE261479", "Transcriptome Analysis", "Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods:  Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 \u00b5M were collected for RNA seq.", null, "pubmed:40053597", null, "DAPT 2", "GSM8144969", null, "source name:hearts|tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DAPT|geo loc name:missing|collection date:missing", "DAPT 2", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix  between treatment samples and wild type samples.", "hearts", "60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 \u03bcM  to 96 hpf.", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer\u2019s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", "Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau\u2019s Buffer at 28 \u00b0C with a photoperiod of 14/10\u2009h.", "tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DAPT", "GSM8144969", "GSM8144969: DAPT 2; Danio rerio; RNA Seq", "GSM8144969 r1", "GSM8144969", "1", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494974", null, null, "DAPT_2_1.fq.gz DAPT_2_2.fq.gz", "fastq fastq", 6920695600.0, 34603478.0, "GSM8144969 r1", "0:100 1:100", "A:1880782056;C:1560368169;G:1581248339;T:1898297036;N:0", 100, 100, null, null, 1880782056, 1560368169, 1581248339, 1898297036, 0, "SRX23938185", "SRS20741666", "SRA1823438", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", 2, 0.93355, 0.93357, 0.10276, 0.10282, 0.67363, 0.67361, 0.51703, 0.52041, 100, 100, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-03-13", "Larval", "Larval", "Heart", "Cardiovascular System"], [30710, "SRR28329753", "SRX23938184", "SRS20741665", "SRP494974", "PRJNA1087264", "Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression", "GSE261479", "Transcriptome Analysis", "Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods:  Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 \u00b5M were collected for RNA seq.", null, "pubmed:40053597", null, "DAPT 1", "GSM8144968", null, "source name:hearts|tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DAPT|geo loc name:missing|collection date:missing", "DAPT 1", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix  between treatment samples and wild type samples.", "hearts", "60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 \u03bcM  to 96 hpf.", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer\u2019s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", "Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau\u2019s Buffer at 28 \u00b0C with a photoperiod of 14/10\u2009h.", "tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DAPT", "GSM8144968", "GSM8144968: DAPT 1; Danio rerio; RNA Seq", "GSM8144968 r1", "GSM8144968", "1", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494974", null, null, "DAPT_1_1.fq.gz DAPT_1_2.fq.gz", "fastq fastq", 6917244000.0, 34586220.0, "GSM8144968 r1", "0:100 1:100", "A:1871550461;C:1566067610;G:1585361217;T:1894264712;N:0", 100, 100, null, null, 1871550461, 1566067610, 1585361217, 1894264712, 0, "SRX23938184", "SRS20741665", "SRA1823438", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", 2, 0.9357, 0.93705, 0.09751, 0.09758, 0.67387, 0.67363, 0.51842, 0.51997, 100, 100, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-03-13", "Larval", "Larval", "Heart", "Cardiovascular System"], [30711, "SRR28329754", "SRX23938183", "SRS20741664", "SRP494974", "PRJNA1087264", "Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression", "GSE261479", "Transcriptome Analysis", "Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods:  Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 \u00b5M were collected for RNA seq.", null, "pubmed:40053597", null, "DMSO 3", "GSM8144967", null, "source name:hearts|tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DMSO|geo loc name:missing|collection date:missing", "DMSO 3", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix  between treatment samples and wild type samples.", "hearts", "60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 \u03bcM  to 96 hpf.", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer\u2019s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", "Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau\u2019s Buffer at 28 \u00b0C with a photoperiod of 14/10\u2009h.", "tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DMSO", "GSM8144967", "GSM8144967: DMSO 3; Danio rerio; RNA Seq", "GSM8144967 r1", "GSM8144967", "1", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494974", null, null, "DMSO_3_2.fq.gz DMSO_3_1.fq.gz", "fastq fastq", 6919708800.0, 34598544.0, "GSM8144967 r1", "0:100 1:100", "A:1894083722;C:1545002324;G:1569342322;T:1911280432;N:0", 100, 100, null, null, 1894083722, 1545002324, 1569342322, 1911280432, 0, "SRX23938183", "SRS20741664", "SRA1823438", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", 2, 0.93873, 0.93836, 0.10256, 0.10261, 0.66068, 0.6616, 0.52724, 0.52601, 100, 100, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-03-13", "Larval", "Larval", "Heart", "Cardiovascular System"], [30712, "SRR28329755", "SRX23938182", "SRS20741663", "SRP494974", "PRJNA1087264", "Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression", "GSE261479", "Transcriptome Analysis", "Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods:  Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 \u00b5M were collected for RNA seq.", null, "pubmed:40053597", null, "DMSO 2", "GSM8144966", null, "source name:hearts|tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DMSO|geo loc name:missing|collection date:missing", "DMSO 2", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix  between treatment samples and wild type samples.", "hearts", "60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 \u03bcM  to 96 hpf.", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer\u2019s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", "Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau\u2019s Buffer at 28 \u00b0C with a photoperiod of 14/10\u2009h.", "tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DMSO", "GSM8144966", "GSM8144966: DMSO 2; Danio rerio; RNA Seq", "GSM8144966 r1", "GSM8144966", "1", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494974", null, null, "DMSO_2_1.fq.gz DMSO_2_2.fq.gz", "fastq fastq", 6902487800.0, 34512439.0, "GSM8144966 r1", "0:100 1:100", "A:1892099736;C:1540950565;G:1559704613;T:1909732886;N:0", 100, 100, null, null, 1892099736, 1540950565, 1559704613, 1909732886, 0, "SRX23938182", "SRS20741663", "SRA1823438", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", 2, 0.93535, 0.93511, 0.10112, 0.10162, 0.66541, 0.66592, 0.51543, 0.51644, 100, 100, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-03-13", "Larval", "Larval", "Heart", "Cardiovascular System"], [30713, "SRR28329756", "SRX23938181", "SRS20741662", "SRP494974", "PRJNA1087264", "Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression", "GSE261479", "Transcriptome Analysis", "Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods:  Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 \u00b5M were collected for RNA seq.", null, "pubmed:40053597", null, "DMSO 1", "GSM8144965", null, "source name:hearts|tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DMSO|geo loc name:missing|collection date:missing", "DMSO 1", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix  between treatment samples and wild type samples.", "hearts", "60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 \u03bcM  to 96 hpf.", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer\u2019s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", "Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau\u2019s Buffer at 28 \u00b0C with a photoperiod of 14/10\u2009h.", "tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DMSO", "GSM8144965", "GSM8144965: DMSO 1; Danio rerio; RNA Seq", "GSM8144965 r1", "GSM8144965", "1", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494974", null, null, "DMSO_1_1.fq.gz DMSO_1_2.fq.gz", "fastq fastq", 6918299800.0, 34591499.0, "GSM8144965 r1", "0:100 1:100", "A:1887082093;C:1551476280;G:1575428027;T:1904313400;N:0", 100, 100, null, null, 1887082093, 1551476280, 1575428027, 1904313400, 0, "SRX23938181", "SRS20741662", "SRA1823438", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", 2, 0.93809, 0.93843, 0.098, 0.09793, 0.66647, 0.66709, 0.53463, 0.52582, 100, 100, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-03-13", "Larval", "Larval", "Heart", "Cardiovascular System"], [31545, "SRR28435452", "SRX24039370", "SRS20832135", "SRP497581", "PRJNA1091566", "The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration", "GSE262351", "Transcriptome Analysis", "The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: Aim: Investigation of the MyD88 signaling in endocardial cells during zebrafish cardiac regeneration. Methods: Endocardial cells sorted from the ETkrt4:EGFPsqet33 1A line at 96 hours post cryoinjury hpci. Conditions: 3 myd88+/+ and 3 myd88 /  samples", null, "pubmed:39271818", null, "myd88 3", "GSM8163706", null, "tissue:endocardial|cell type:endocardial|genotype:myd88 / |time:96 hpci|geo loc name:missing|collection date:missing", "myd88 3", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 109 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Assembly: danRer11 Supplementary files format and content: The tab delimited matrix shows DESeq normalized gene counts.", "endocardial", null, "RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.", null, "cell type:endocardial|genotype:myd88 / |time:96 hpci", "GSM8163706", "GSM8163706: myd88 3; Danio rerio; RNA Seq", "GSM8163706 r1", "GSM8163706", "1", "RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP497581", null, "loader:fastq load.py", "myd88_3_1.fq.gz myd88_3_2.fq.gz", "fastq fastq", 6626254800.0, 22087516.0, "GSM8163706 r1", "0:150 1:150", "A:1858405504;C:1462442884;G:1470757827;T:1834548220;N:100365", 150, 150, null, null, 1858405504, 1462442884, 1470757827, 1834548220, 100365, "SRX24039370", "SRS20832135", "SRA1832826", "Bioinformatics, Max-Planck-Institute for Heart and Lung Research", "Bioinformatics, Max-Planck-Institute for Heart and Lung Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-03-25", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31546, "SRR28435455", "SRX24039369", "SRS20832134", "SRP497581", "PRJNA1091566", "The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration", "GSE262351", "Transcriptome Analysis", "The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: Aim: Investigation of the MyD88 signaling in endocardial cells during zebrafish cardiac regeneration. Methods: Endocardial cells sorted from the ETkrt4:EGFPsqet33 1A line at 96 hours post cryoinjury hpci. Conditions: 3 myd88+/+ and 3 myd88 /  samples", null, "pubmed:39271818", null, "myd88 2", "GSM8163705", null, "tissue:endocardial|cell type:endocardial|genotype:myd88 / |time:96 hpci|geo loc name:missing|collection date:missing", "myd88 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 109 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Assembly: danRer11 Supplementary files format and content: The tab delimited matrix shows DESeq normalized gene counts.", "endocardial", null, "RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.", null, "cell type:endocardial|genotype:myd88 / |time:96 hpci", "GSM8163705", "GSM8163705: myd88 2; Danio rerio; RNA Seq", "GSM8163705 r1", "GSM8163705", "1", "RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP497581", null, "loader:fastq load.py", "myd88_2_1.fq.gz myd88_2_2.fq.gz", "fastq fastq", 6586163100.0, 21953877.0, "GSM8163705 r1", "0:150 1:150", "A:1856129657;C:1440403994;G:1451543521;T:1837982507;N:103421", 150, 150, null, null, 1856129657, 1440403994, 1451543521, 1837982507, 103421, "SRX24039369", "SRS20832134", "SRA1832826", "Bioinformatics, Max-Planck-Institute for Heart and Lung Research", "Bioinformatics, Max-Planck-Institute for Heart and Lung Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-03-25", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31547, "SRR28435453", "SRX24039368", "SRS20832133", "SRP497581", "PRJNA1091566", "The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration", "GSE262351", "Transcriptome Analysis", "The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: Aim: Investigation of the MyD88 signaling in endocardial cells during zebrafish cardiac regeneration. Methods: Endocardial cells sorted from the ETkrt4:EGFPsqet33 1A line at 96 hours post cryoinjury hpci. Conditions: 3 myd88+/+ and 3 myd88 /  samples", null, "pubmed:39271818", null, "myd88 1", "GSM8163704", null, "tissue:endocardial|cell type:endocardial|genotype:myd88 / |time:96 hpci|geo loc name:missing|collection date:missing", "myd88 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 109 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Assembly: danRer11 Supplementary files format and content: The tab delimited matrix shows DESeq normalized gene counts.", "endocardial", null, "RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.", null, "cell type:endocardial|genotype:myd88 / |time:96 hpci", "GSM8163704", "GSM8163704: myd88 1; Danio rerio; RNA Seq", "GSM8163704 r1", "GSM8163704", "1", "RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP497581", null, "loader:fastq load.py", "myd88_1_1.fq.gz myd88_1_2.fq.gz", "fastq fastq", 6586212900.0, 21954043.0, "GSM8163704 r1", "0:150 1:150", "A:1835825607;C:1467677697;G:1474870953;T:1807740616;N:98027", 150, 150, null, null, 1835825607, 1467677697, 1474870953, 1807740616, 98027, "SRX24039368", "SRS20832133", "SRA1832826", "Bioinformatics, Max-Planck-Institute for Heart and Lung Research", "Bioinformatics, Max-Planck-Institute for Heart and Lung Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-03-25", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31548, "SRR28435454", "SRX24039367", "SRS20832132", "SRP497581", "PRJNA1091566", "The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration", "GSE262351", "Transcriptome Analysis", "The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: Aim: Investigation of the MyD88 signaling in endocardial cells during zebrafish cardiac regeneration. Methods: Endocardial cells sorted from the ETkrt4:EGFPsqet33 1A line at 96 hours post cryoinjury hpci. Conditions: 3 myd88+/+ and 3 myd88 /  samples", null, "pubmed:39271818", null, "WT 3", "GSM8163703", null, "tissue:endocardial|cell type:endocardial|genotype:myd88+/+|time:96 hpci|geo loc name:missing|collection date:missing", "WT 3", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 109 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Assembly: danRer11 Supplementary files format and content: The tab delimited matrix shows DESeq normalized gene counts.", "endocardial", null, "RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.", null, "cell type:endocardial|genotype:myd88+/+|time:96 hpci", "GSM8163703", "GSM8163703: WT 3; Danio rerio; RNA Seq", "GSM8163703 r1", "GSM8163703", "1", "RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP497581", null, "loader:fastq load.py", "WT_3_1.fq.gz WT_3_2.fq.gz", "fastq fastq", 6554345400.0, 21847818.0, "GSM8163703 r1", "0:150 1:150", "A:1829151207;C:1459298563;G:1466145928;T:1799650897;N:98805", 150, 150, null, null, 1829151207, 1459298563, 1466145928, 1799650897, 98805, "SRX24039367", "SRS20832132", "SRA1832826", "Bioinformatics, Max-Planck-Institute for Heart and Lung Research", "Bioinformatics, Max-Planck-Institute for Heart and Lung Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-03-25", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31549, "SRR28435456", "SRX24039366", "SRS20832131", "SRP497581", "PRJNA1091566", "The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration", "GSE262351", "Transcriptome Analysis", "The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: Aim: Investigation of the MyD88 signaling in endocardial cells during zebrafish cardiac regeneration. Methods: Endocardial cells sorted from the ETkrt4:EGFPsqet33 1A line at 96 hours post cryoinjury hpci. Conditions: 3 myd88+/+ and 3 myd88 /  samples", null, "pubmed:39271818", null, "WT 2", "GSM8163702", null, "tissue:endocardial|cell type:endocardial|genotype:myd88+/+|time:96 hpci|geo loc name:missing|collection date:missing", "WT 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 109 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Assembly: danRer11 Supplementary files format and content: The tab delimited matrix shows DESeq normalized gene counts.", "endocardial", null, "RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.", null, "cell type:endocardial|genotype:myd88+/+|time:96 hpci", "GSM8163702", "GSM8163702: WT 2; Danio rerio; RNA Seq", "GSM8163702 r1", "GSM8163702", "1", "RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP497581", null, "loader:fastq load.py", "WT_2_1.fq.gz WT_2_2.fq.gz", "fastq fastq", 6440692500.0, 21468975.0, "GSM8163702 r1", "0:150 1:150", "A:1797022330;C:1433189990;G:1440263369;T:1770115464;N:101347", 150, 150, null, null, 1797022330, 1433189990, 1440263369, 1770115464, 101347, "SRX24039366", "SRS20832131", "SRA1832826", "Bioinformatics, Max-Planck-Institute for Heart and Lung Research", "Bioinformatics, Max-Planck-Institute for Heart and Lung Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-03-25", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31550, "SRR28435457", "SRX24039365", "SRS20832130", "SRP497581", "PRJNA1091566", "The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration", "GSE262351", "Transcriptome Analysis", "The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: Aim: Investigation of the MyD88 signaling in endocardial cells during zebrafish cardiac regeneration. Methods: Endocardial cells sorted from the ETkrt4:EGFPsqet33 1A line at 96 hours post cryoinjury hpci. Conditions: 3 myd88+/+ and 3 myd88 /  samples", null, "pubmed:39271818", null, "WT 1", "GSM8163701", null, "tissue:endocardial|cell type:endocardial|genotype:myd88+/+|time:96 hpci|geo loc name:missing|collection date:missing", "WT 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 109 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Assembly: danRer11 Supplementary files format and content: The tab delimited matrix shows DESeq normalized gene counts.", "endocardial", null, "RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.", null, "cell type:endocardial|genotype:myd88+/+|time:96 hpci", "GSM8163701", "GSM8163701: WT 1; Danio rerio; RNA Seq", "GSM8163701 r1", "GSM8163701", "1", "RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP497581", null, "loader:fastq load.py", "WT_1_1.fq.gz WT_1_2.fq.gz", "fastq fastq", 6343747500.0, 21145825.0, "GSM8163701 r1", "0:150 1:150", "A:1783890425;C:1396753566;G:1403241010;T:1759774134;N:88365", 150, 150, null, null, 1783890425, 1396753566, 1403241010, 1759774134, 88365, "SRX24039365", "SRS20832130", "SRA1832826", "Bioinformatics, Max-Planck-Institute for Heart and Lung Research", "Bioinformatics, Max-Planck-Institute for Heart and Lung Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-03-25", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31896, "SRR28745432", "SRX24311225", "SRS21073227", "SRP502845", "PRJNA1102356", "flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response", "GSE264406", "Transcriptome Analysis", "VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.", null, "pubmed:39612288", null, "wild type heart  96 hours post cryoinjury 3", "GSM8217704", null, "source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "wild type heart  96 hours post cryoinjury 3", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix", "heart ventricle border zone and injured area", null, "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury", "GSM8217704", "GSM8217704: wild type heart  96 hours post cryoinjury 3; Danio rerio; RNA Seq", "GSM8217704 r1", "GSM8217704", "1", "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "loader:fastq load.py", "E23_4173_Armaad_Lib_WT3_R1.fastq.gz", "fastq", 3257983192.0, 47556048.0, "GSM8217704 r1", "0:68.51", "A:848972796;C:741588101;G:760680137;T:905607069;N:1135089", 68, null, null, null, 848972796, 741588101, 760680137, 905607069, 1135089, "SRX24311225", "SRS21073227", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.94185, null, 0.087, null, 0.72478, null, 0.50388, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-04-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31897, "SRR28745433", "SRX24311224", "SRS21073229", "SRP502845", "PRJNA1102356", "flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response", "GSE264406", "Transcriptome Analysis", "VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.", null, "pubmed:39612288", null, "wild type heart  96 hours post cryoinjury 2", "GSM8217703", null, "source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "wild type heart  96 hours post cryoinjury 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix", "heart ventricle border zone and injured area", null, "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury", "GSM8217703", "GSM8217703: wild type heart  96 hours post cryoinjury 2; Danio rerio; RNA Seq", "GSM8217703 r1", "GSM8217703", "1", "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "loader:fastq load.py", "E23_4173_Armaad_Lib_WT2_R1.fastq.gz", "fastq", 3864619254.0, 56519751.0, "GSM8217703 r1", "0:68.38", "A:1003402543;C:880721584;G:903469106;T:1075304136;N:1721885", 68, null, null, null, 1003402543, 880721584, 903469106, 1075304136, 1721885, "SRX24311224", "SRS21073229", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.93928, null, 0.08915, null, 0.72348, null, 0.49993, null, 71, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-04-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31898, "SRR28745434", "SRX24311223", "SRS21073228", "SRP502845", "PRJNA1102356", "flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response", "GSE264406", "Transcriptome Analysis", "VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.", null, "pubmed:39612288", null, "wild type heart  96 hours post cryoinjury 1", "GSM8217702", null, "source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "wild type heart  96 hours post cryoinjury 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix", "heart ventricle border zone and injured area", null, "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury", "GSM8217702", "GSM8217702: wild type heart  96 hours post cryoinjury 1; Danio rerio; RNA Seq", "GSM8217702 r1", "GSM8217702", "1", "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "loader:fastq load.py", "E23_4173_Armaad_Lib_WT1_R1.fastq.gz", "fastq", 3571478400.0, 52133215.0, "GSM8217702 r1", "0:68.51", "A:928171678;C:814216251;G:835024543;T:992630615;N:1435313", 68, null, null, null, 928171678, 814216251, 835024543, 992630615, 1435313, "SRX24311223", "SRS21073228", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.94111, null, 0.08647, null, 0.72922, null, 0.50812, null, 42, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-04-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31899, "SRR28745435", "SRX24311222", "SRS21073226", "SRP502845", "PRJNA1102356", "flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response", "GSE264406", "Transcriptome Analysis", "VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.", null, "pubmed:39612288", null, "flt1 mutant heart  96 hours post cryoinjury 3", "GSM8217701", null, "source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "flt1 mutant heart  96 hours post cryoinjury 3", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix", "heart ventricle border zone and injured area", null, "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury", "GSM8217701", "GSM8217701: flt1 mutant heart  96 hours post cryoinjury 3; Danio rerio; RNA Seq", "GSM8217701 r1", "GSM8217701", "1", "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "loader:fastq load.py", "E23_4173_Armaad_Lib_FLT_MUT3_R1.fastq.gz", "fastq", 4085359270.0, 59673604.0, "GSM8217701 r1", "0:68.46", "A:1050667797;C:938174838;G:953989485;T:1140941596;N:1585554", 68, null, null, null, 1050667797, 938174838, 953989485, 1140941596, 1585554, "SRX24311222", "SRS21073226", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.94035, null, 0.08631, null, 0.72376, null, 0.49828, null, 69, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-04-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31900, "SRR28745436", "SRX24311221", "SRS21073225", "SRP502845", "PRJNA1102356", "flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response", "GSE264406", "Transcriptome Analysis", "VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.", null, "pubmed:39612288", null, "flt1 mutant heart  96 hours post cryoinjury 2", "GSM8217700", null, "source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "flt1 mutant heart  96 hours post cryoinjury 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix", "heart ventricle border zone and injured area", null, "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury", "GSM8217700", "GSM8217700: flt1 mutant heart  96 hours post cryoinjury 2; Danio rerio; RNA Seq", "GSM8217700 r1", "GSM8217700", "1", "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "loader:fastq load.py", "E23_4173_Armaad_Lib_FLT_MUT2_R1.fastq.gz", "fastq", 4696922408.0, 68645737.0, "GSM8217700 r1", "0:68.42", "A:1220019708;C:1072448104;G:1106194472;T:1296618556;N:1641568", 68, null, null, null, 1220019708, 1072448104, 1106194472, 1296618556, 1641568, "SRX24311221", "SRS21073225", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.94205, null, 0.08792, null, 0.72543, null, 0.50566, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-04-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31901, "SRR28745437", "SRX24311220", "SRS21073224", "SRP502845", "PRJNA1102356", "flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response", "GSE264406", "Transcriptome Analysis", "VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.", null, "pubmed:39612288", null, "flt1 mutant heart  96 hours post cryoinjury 1", "GSM8217699", null, "source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "flt1 mutant heart  96 hours post cryoinjury 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix", "heart ventricle border zone and injured area", null, "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury", "GSM8217699", "GSM8217699: flt1 mutant heart  96 hours post cryoinjury 1; Danio rerio; RNA Seq", "GSM8217699 r1", "GSM8217699", "1", "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "loader:fastq load.py", "E23_4173_Armaad_Lib_FLT_MUT1_R1.fastq.gz", "fastq", 2897934017.0, 42657803.0, "GSM8217699 r1", "0:67.93", "A:749045495;C:662930035;G:683478060;T:800853726;N:1626701", 67, null, null, null, 749045495, 662930035, 683478060, 800853726, 1626701, "SRX24311220", "SRS21073224", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.94107, null, 0.08304, null, 0.72579, null, 0.50482, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-04-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [32629, "SRR29382473", "SRX24896629", "SRS21602926", "SRP513565", "PRJNA1123307", "To identify differentially expressed genes in ventricular tissue between wildtype control and the 6 mpf mtorxu015/+ mutant  Tgcmlc2:tfeb transgenic zebrafish at six months.", "GSE269725", "Transcriptome Analysis", "To seek molecular mechanisms underlying the mechanisms of mutant genotypes by comparing them witht he wild types  we performed whole transcriptome RNA sequencing experiments using ventricular tissue isolated from 6 mpf mtorxu015/+ mutant  Tgcmlc2:tfeb transgenic zebrafish and corresponding WT siblings. Overall design: Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings.", null, null, null, "tg3", "GSM8325761", null, "source name:Heart|tissue:Heart|genotype:Tgcmlc2:tfeb transgenic|geo loc name:missing|collection date:missing", "tg3", "Image analysis and base calling were conducted by the HiSeq Control Software HCS. Raw sequence data .bcl files generated from Illumina HiSeq was converted into fastq files and de multiplexed using Illumina's bcl2fastq 2.17 software. Sequence read will be trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads will be mapped to the ZV9 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Assembly: Danio rerio.GRCz11.cdna.all.fa Supplementary files format and content: merged gene counts.txt", "Heart", null, "Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings. Five ventricles were pooled as one sample and three biological replicates for each genotype were sequenced using the HiSeq 2000 platform. Illumina with a 50 bp paired end sequencing protocol in the Mayo Clinic DNA Sequencing Core Facility", null, "tissue:Heart|genotype:Tgcmlc2:tfeb transgenic", "GSM8325761", "GSM8325761: tg3; Danio rerio; RNA Seq", "GSM8325761 r1", "GSM8325761", "1", "Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings. Five ventricles were pooled as one sample and three biological replicates for each genotype were sequenced using the HiSeq 2000 platform. Illumina with a 50 bp paired end sequencing protocol in the Mayo Clinic DNA Sequencing Core Facility", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP513565", null, null, "tgTFEB-3.FCC83VDACXX_L2_R2_IACTTGA.fastq.gz tgTFEB-3.FCC83VDACXX_L2_R1_IACTTGA.fastq.gz", "fastq fastq", 4329815748.0, 42449174.0, "GSM8325761 r1", "0:51 1:51", "A:1142130932;C:1032964058;G:1007903605;T:1146154372;N:662781", 51, 51, null, null, 1142130932, 1032964058, 1007903605, 1146154372, 662781, "SRX24896629", "SRS21602926", "SRA1897306", "University of Maryland", "University of Maryland", 2, 0.93676, 0.93675, 0.07682, 0.07757, 0.77027, 0.77293, 0.50098, 0.5234, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-06-12", "Adult", "Adult", "Heart", "Cardiovascular System"], [32630, "SRR29382474", "SRX24896628", "SRS21602921", "SRP513565", "PRJNA1123307", "To identify differentially expressed genes in ventricular tissue between wildtype control and the 6 mpf mtorxu015/+ mutant  Tgcmlc2:tfeb transgenic zebrafish at six months.", "GSE269725", "Transcriptome Analysis", "To seek molecular mechanisms underlying the mechanisms of mutant genotypes by comparing them witht he wild types  we performed whole transcriptome RNA sequencing experiments using ventricular tissue isolated from 6 mpf mtorxu015/+ mutant  Tgcmlc2:tfeb transgenic zebrafish and corresponding WT siblings. Overall design: Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings.", null, null, null, "tg2", "GSM8325760", null, "source name:Heart|tissue:Heart|genotype:Tgcmlc2:tfeb transgenic|geo loc name:missing|collection date:missing", "tg2", "Image analysis and base calling were conducted by the HiSeq Control Software HCS. Raw sequence data .bcl files generated from Illumina HiSeq was converted into fastq files and de multiplexed using Illumina's bcl2fastq 2.17 software. Sequence read will be trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads will be mapped to the ZV9 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Assembly: Danio rerio.GRCz11.cdna.all.fa Supplementary files format and content: merged gene counts.txt", "Heart", null, "Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings. Five ventricles were pooled as one sample and three biological replicates for each genotype were sequenced using the HiSeq 2000 platform. Illumina with a 50 bp paired end sequencing protocol in the Mayo Clinic DNA Sequencing Core Facility", null, "tissue:Heart|genotype:Tgcmlc2:tfeb transgenic", "GSM8325760", "GSM8325760: tg2; Danio rerio; RNA Seq", "GSM8325760 r1", "GSM8325760", "1", "Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings. Five ventricles were pooled as one sample and three biological replicates for each genotype were sequenced using the HiSeq 2000 platform. 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Overall design: Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings.", null, null, null, "tg1", "GSM8325759", null, "source name:Heart|tissue:Heart|genotype:Tgcmlc2:tfeb transgenic|geo loc name:missing|collection date:missing", "tg1", "Image analysis and base calling were conducted by the HiSeq Control Software HCS. Raw sequence data .bcl files generated from Illumina HiSeq was converted into fastq files and de multiplexed using Illumina's bcl2fastq 2.17 software. Sequence read will be trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads will be mapped to the ZV9 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Assembly: Danio rerio.GRCz11.cdna.all.fa Supplementary files format and content: merged gene counts.txt", "Heart", null, "Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings. Five ventricles were pooled as one sample and three biological replicates for each genotype were sequenced using the HiSeq 2000 platform. Illumina with a 50 bp paired end sequencing protocol in the Mayo Clinic DNA Sequencing Core Facility", null, "tissue:Heart|genotype:Tgcmlc2:tfeb transgenic", "GSM8325759", "GSM8325759: tg1; Danio rerio; RNA Seq", "GSM8325759 r1", "GSM8325759", "1", "Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings. Five ventricles were pooled as one sample and three biological replicates for each genotype were sequenced using the HiSeq 2000 platform. 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Overall design: Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings.", null, null, null, "mtor3", "GSM8325758", null, "source name:Heart|tissue:Heart|genotype:mtorxu015/+ mutant|geo loc name:missing|collection date:missing", "mtor3", "Image analysis and base calling were conducted by the HiSeq Control Software HCS. Raw sequence data .bcl files generated from Illumina HiSeq was converted into fastq files and de multiplexed using Illumina's bcl2fastq 2.17 software. Sequence read will be trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads will be mapped to the ZV9 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Assembly: Danio rerio.GRCz11.cdna.all.fa Supplementary files format and content: merged gene counts.txt", "Heart", null, "Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings. Five ventricles were pooled as one sample and three biological replicates for each genotype were sequenced using the HiSeq 2000 platform. Illumina with a 50 bp paired end sequencing protocol in the Mayo Clinic DNA Sequencing Core Facility", null, "tissue:Heart|genotype:mtorxu015/+ mutant", "GSM8325758", "GSM8325758: mtor3; Danio rerio; RNA Seq", "GSM8325758 r1", "GSM8325758", "1", "Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings. Five ventricles were pooled as one sample and three biological replicates for each genotype were sequenced using the HiSeq 2000 platform. Illumina with a 50 bp paired end sequencing protocol in the Mayo Clinic DNA Sequencing Core Facility", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP513565", null, null, "mTOR_het-3.FCC83VDACXX_L2_R1_IATTCCT.fastq.gz mTOR_het-3.FCC83VDACXX_L2_R2_IATTCCT.fastq.gz", "fastq fastq", 5399672124.0, 52937962.0, "GSM8325758 r1", "0:51 1:51", "A:1426491266;C:1289402352;G:1254574572;T:1428381829;N:822105", 51, 51, null, null, 1426491266, 1289402352, 1254574572, 1428381829, 822105, "SRX24896626", "SRS21602925", "SRA1897306", "University of Maryland", "University of Maryland", 2, 0.94083, 0.93917, 0.0727, 0.07261, 0.77108, 0.7738, 0.46987, 0.46779, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-06-12", "Adult", "Adult", "Heart", "Cardiovascular System"], [32633, "SRR29382477", "SRX24896625", "SRS21602924", "SRP513565", "PRJNA1123307", "To identify differentially expressed genes in ventricular tissue between wildtype control and the 6 mpf mtorxu015/+ mutant  Tgcmlc2:tfeb transgenic zebrafish at six months.", "GSE269725", "Transcriptome Analysis", "To seek molecular mechanisms underlying the mechanisms of mutant genotypes by comparing them witht he wild types  we performed whole transcriptome RNA sequencing experiments using ventricular tissue isolated from 6 mpf mtorxu015/+ mutant  Tgcmlc2:tfeb transgenic zebrafish and corresponding WT siblings. Overall design: Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings.", null, null, null, "mtor2", "GSM8325757", null, "source name:Heart|tissue:Heart|genotype:mtorxu015/+ mutant|geo loc name:missing|collection date:missing", "mtor2", "Image analysis and base calling were conducted by the HiSeq Control Software HCS. Raw sequence data .bcl files generated from Illumina HiSeq was converted into fastq files and de multiplexed using Illumina's bcl2fastq 2.17 software. Sequence read will be trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads will be mapped to the ZV9 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Assembly: Danio rerio.GRCz11.cdna.all.fa Supplementary files format and content: merged gene counts.txt", "Heart", null, "Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings. Five ventricles were pooled as one sample and three biological replicates for each genotype were sequenced using the HiSeq 2000 platform. Illumina with a 50 bp paired end sequencing protocol in the Mayo Clinic DNA Sequencing Core Facility", null, "tissue:Heart|genotype:mtorxu015/+ mutant", "GSM8325757", "GSM8325757: mtor2; Danio rerio; RNA Seq", "GSM8325757 r1", "GSM8325757", "1", "Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings. Five ventricles were pooled as one sample and three biological replicates for each genotype were sequenced using the HiSeq 2000 platform. 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Overall design: Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings.", null, null, null, "mtor1", "GSM8325756", null, "source name:Heart|tissue:Heart|genotype:mtorxu015/+ mutant|geo loc name:missing|collection date:missing", "mtor1", "Image analysis and base calling were conducted by the HiSeq Control Software HCS. Raw sequence data .bcl files generated from Illumina HiSeq was converted into fastq files and de multiplexed using Illumina's bcl2fastq 2.17 software. Sequence read will be trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads will be mapped to the ZV9 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Assembly: Danio rerio.GRCz11.cdna.all.fa Supplementary files format and content: merged gene counts.txt", "Heart", null, "Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings. Five ventricles were pooled as one sample and three biological replicates for each genotype were sequenced using the HiSeq 2000 platform. Illumina with a 50 bp paired end sequencing protocol in the Mayo Clinic DNA Sequencing Core Facility", null, "tissue:Heart|genotype:mtorxu015/+ mutant", "GSM8325756", "GSM8325756: mtor1; Danio rerio; RNA Seq", "GSM8325756 r1", "GSM8325756", "1", "Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings. Five ventricles were pooled as one sample and three biological replicates for each genotype were sequenced using the HiSeq 2000 platform. 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Overall design: Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings.", null, null, null, "WT3", "GSM8325755", null, "source name:Heart|tissue:Heart|genotype:WT|geo loc name:missing|collection date:missing", "WT3", "Image analysis and base calling were conducted by the HiSeq Control Software HCS. Raw sequence data .bcl files generated from Illumina HiSeq was converted into fastq files and de multiplexed using Illumina's bcl2fastq 2.17 software. Sequence read will be trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads will be mapped to the ZV9 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Assembly: Danio rerio.GRCz11.cdna.all.fa Supplementary files format and content: merged gene counts.txt", "Heart", null, "Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings. Five ventricles were pooled as one sample and three biological replicates for each genotype were sequenced using the HiSeq 2000 platform. Illumina with a 50 bp paired end sequencing protocol in the Mayo Clinic DNA Sequencing Core Facility", null, "tissue:Heart|genotype:WT", "GSM8325755", "GSM8325755: WT3; Danio rerio; RNA Seq", "GSM8325755 r1", "GSM8325755", "1", "Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings. Five ventricles were pooled as one sample and three biological replicates for each genotype were sequenced using the HiSeq 2000 platform. 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"expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"experiment.library_selection\" = :p0 and \"technology\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "cDNA", "p1": "unknown", "p2": "Heart"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 846, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 846, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart", "results": [{"value": "cDNA", "label": "cDNA", "count": 846, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=unknown&tissue_curation=Heart", "selected": true}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 471, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart&experiment.library_layout=PAIRED", "selected": false}, {"value": "SINGLE", "label": "SINGLE", "count": 375, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart&experiment.library_layout=SINGLE", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 812, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart&experiment.platform=ILLUMINA", "selected": false}, {"value": "BGISEQ", "label": "BGISEQ", "count": 24, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart&experiment.platform=BGISEQ", "selected": false}, {"value": "ELEMENT", "label": "ELEMENT", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart&experiment.platform=ELEMENT", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart", "results": [{"value": "Adult", "label": "Adult", "count": 557, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart&devstage_curation_coarse=Adult", "selected": false}, {"value": "Embryo", "label": "Embryo", "count": 152, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart&devstage_curation_coarse=Embryo", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 71, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart&devstage_curation_coarse=Undetermined", "selected": false}, {"value": "Larval", "label": "Larval", "count": 52, "toggle_url": 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"count": 133, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart&devstage_curation=Undetermined", "selected": false}, {"value": "Hatching", "label": "Hatching", "count": 86, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart&devstage_curation=Hatching", "selected": false}, {"value": "Larval", "label": "Larval", "count": 46, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart&devstage_curation=Larval", "selected": false}, {"value": "Segmentation", "label": "Segmentation", "count": 23, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart&devstage_curation=Segmentation", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 18, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart&devstage_curation=Multi-stage", "selected": false}, {"value": "Pharyngula", "label": "Pharyngula", "count": 13, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart&devstage_curation=Pharyngula", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&technology=unknown&tissue_curation=Heart", "results": [{"value": "Cardiovascular System", "label": "Cardiovascular System", "count": 846, "toggle_url": 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