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890 rows where experiment.library_layout = "PAIRED", technology = "unknown" and tissue_curation_coarse = "Cardiovascular System"

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experiment.library_selection 10

devstage_curation 8

devstage_curation_coarse 5

tissue_curation 3

experiment.platform 2

tissue_curation_coarse 1

  • Cardiovascular System · 890 ✖

technology 1

  • unknown · 890 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_layout 1

  • PAIRED · 890 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
226 226 DRR162515 DRX153134 DRS083195 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.       heart sample from 39 mpf zebrafish replicate4 SAMD00152463   sample name:h39 5|age:39 month|biological replicate:4|tissue:heart                 Illumina HiSeq 2000 paired end sequencing of SAMD00152463 DRX153134 1 1 Illumina TruSeq Stranded mRNA HT Kit   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 SAMD00152463       752785200.0 3763926.0 DRR162515 0:100 1:100 A:211753297;C:164230605;G:164002975;T:211653858;N:1144465 100 100     211753297 164230605 164002975 211653858 1144465 DRX153134 DRS083195 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 0.94694 0.92403 0.08673 0.0834 0.76676 0.77494 0.55153 0.55428 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Heart Cardiovascular System
227 227 DRR162514 DRX153133 DRS083194 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.       heart sample from 39 mpf zebrafish replicate3 SAMD00152462   sample name:h39 4|age:39 month|biological replicate:3|tissue:heart                 Illumina HiSeq 2000 paired end sequencing of SAMD00152462 DRX153133 1 1 Illumina TruSeq Stranded mRNA HT Kit   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 SAMD00152462       679062000.0 3395310.0 DRR162514 0:100 1:100 A:196564583;C:142498995;G:143087462;T:195785946;N:1125014 100 100     196564583 142498995 143087462 195785946 1125014 DRX153133 DRS083194 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 0.93382 0.90845 0.09509 0.09064 0.74959 0.75716 0.54651 0.55443 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Heart Cardiovascular System
228 228 DRR162513 DRX153132 DRS083193 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.       heart sample from 39 mpf zebrafish replicate2 SAMD00152461   sample name:h39 3|age:39 month|biological replicate:2|tissue:heart                 Illumina HiSeq 2000 paired end sequencing of SAMD00152461 DRX153132 1 1 Illumina TruSeq Stranded mRNA HT Kit   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 SAMD00152461       820363600.0 4101818.0 DRR162513 0:100 1:100 A:216665257;C:194340343;G:194565546;T:214750864;N:41590 100 100     216665257 194340343 194565546 214750864 41590 DRX153132 DRS083193 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 0.96835 0.9597 0.05737 0.05723 0.77518 0.78977 0.52379 0.52345 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Heart Cardiovascular System
229 229 DRR162512 DRX153131 DRS083192 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.       heart sample from 39 mpf zebrafish replicate1 SAMD00152460   sample name:h39 2|age:39 month|biological replicate:1|tissue:heart                 Illumina HiSeq 2000 paired end sequencing of SAMD00152460 DRX153131 1 1 Illumina TruSeq Stranded mRNA HT Kit   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 SAMD00152460       865257400.0 4326287.0 DRR162512 0:100 1:100 A:232463535;C:201007012;G:201960678;T:229782957;N:43218 100 100     232463535 201007012 201960678 229782957 43218 DRX153131 DRS083192 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 0.96533 0.95132 0.05078 0.04891 0.79961 0.80204 0.5113 0.51569 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Heart Cardiovascular System
230 230 DRR162511 DRX153130 DRS083191 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.       heart sample from 16 mpf zebrafish replicate5 SAMD00152459   sample name:h16 5|age:16 month|biological replicate:5|tissue:heart                 Illumina HiSeq 2000 paired end sequencing of SAMD00152459 DRX153130 1 1 Illumina TruSeq Stranded mRNA HT Kit   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 SAMD00152459       719278200.0 3596391.0 DRR162511 0:100 1:100 A:208319036;C:151385486;G:151714770;T:207822080;N:36828 100 100     208319036 151385486 151714770 207822080 36828 DRX153130 DRS083191 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 0.95229 0.95465 0.0764 0.07543 0.80056 0.80229 0.51533 0.5793 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Heart Cardiovascular System
231 231 DRR162510 DRX153129 DRS083190 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.       heart sample from 16 mpf zebrafish replicate4 SAMD00152458   sample name:h16 4|age:16 month|biological replicate:4|tissue:heart                 Illumina HiSeq 2000 paired end sequencing of SAMD00152458 DRX153129 1 1 Illumina TruSeq Stranded mRNA HT Kit   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 SAMD00152458       826575600.0 4132878.0 DRR162510 0:100 1:100 A:248945884;C:164298731;G:163783086;T:249505745;N:42154 100 100     248945884 164298731 163783086 249505745 42154 DRX153129 DRS083190 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 0.92443 0.9204 0.12773 0.1248 0.75702 0.75948 0.55913 0.57701 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Heart Cardiovascular System
232 232 DRR162509 DRX153128 DRS083189 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.       heart sample from 16 mpf zebrafish replicate3 SAMD00152457   sample name:h16 3|age:16 month|biological replicate:3|tissue:heart                 Illumina HiSeq 2000 paired end sequencing of SAMD00152457 DRX153128 1 1 Illumina TruSeq Stranded mRNA HT Kit   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 SAMD00152457       1094115600.0 5470578.0 DRR162509 0:100 1:100 A:323187964;C:223739793;G:223873492;T:323258173;N:56178 100 100     323187964 223739793 223873492 323258173 56178 DRX153128 DRS083189 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 0.94683 0.94429 0.08329 0.08231 0.78845 0.78875 0.59669 0.60756 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Heart Cardiovascular System
233 233 DRR162508 DRX153127 DRS083188 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.       heart sample from 16 mpf zebrafish replicate2 SAMD00152456   sample name:h16 2|age:16 month|biological replicate:2|tissue:heart                 Illumina HiSeq 2000 paired end sequencing of SAMD00152456 DRX153127 1 1 Illumina TruSeq Stranded mRNA HT Kit   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 SAMD00152456       1020794600.0 5103973.0 DRR162508 0:100 1:100 A:308506490;C:201790189;G:201599005;T:308845325;N:53591 100 100     308506490 201790189 201599005 308845325 53591 DRX153127 DRS083188 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 0.93523 0.93011 0.10853 0.10682 0.77727 0.77841 0.5927 0.59624 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Heart Cardiovascular System
234 234 DRR162507 DRX153126 DRS083187 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.       heart sample from 16 mpf zebrafish replicate1 SAMD00152455   sample name:h16 1|age:16 month|biological replicate:1|tissue:heart                 Illumina HiSeq 2000 paired end sequencing of SAMD00152455 DRX153126 1 1 Illumina TruSeq Stranded mRNA HT Kit   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 SAMD00152455       733044200.0 3665221.0 DRR162507 0:100 1:100 A:217522605;C:148795881;G:149576712;T:217109635;N:39367 100 100     217522605 148795881 149576712 217109635 39367 DRX153126 DRS083187 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 0.94337 0.92685 0.08628 0.08365 0.78147 0.78366 0.61098 0.61073 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Heart Cardiovascular System
235 235 DRR162506 DRX153125 DRS083186 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.       heart sample from 7 mpf zebrafish replicate5 SAMD00152454   sample name:h07 5|age:7 month|biological replicate:5|tissue:heart                 Illumina HiSeq 2000 paired end sequencing of SAMD00152454 DRX153125 1 1 Illumina TruSeq Stranded mRNA HT Kit   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       979233200.0 4896166.0 DRR162506 0:100 1:100 A:249561707;C:239388088;G:240240872;T:248407989;N:1634544 100 100     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   Japan 2018-12-24 Adult Adult Heart Cardiovascular System
236 236 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.       heart sample from 7 mpf zebrafish replicate4 SAMD00152453   sample name:h07 4|age:7 month|biological replicate:4|tissue:heart                 Illumina HiSeq 2000 paired end sequencing of SAMD00152453 DRX153124 1 1 Illumina TruSeq Stranded mRNA HT Kit   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       633922400.0 3169612.0 DRR162505 0:100 1:100 A:158236352;C:158464487;G:159505789;T:156692659;N:1023113 100 100     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   Japan 2018-12-24 Adult Adult Heart Cardiovascular System
237 237 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.       heart sample from 7 mpf zebrafish replicate3 SAMD00152452   sample name:h07 3|age:7 month|biological replicate:3|tissue:heart                 Illumina HiSeq 2000 paired end sequencing of SAMD00152452 DRX153123 1 1 Illumina TruSeq Stranded mRNA HT Kit   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       3134971400.0 15674857.0 DRR162504 0:100 1:100 A:848586113;C:717201130;G:718012934;T:846124340;N:5046883 100 100     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   Japan 2018-12-24 Adult Adult Heart Cardiovascular System
238 238 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.       heart sample from 7 mpf zebrafish replicate2 SAMD00152451   sample name:h07 2|age:7 month|biological replicate:2|tissue:heart                 Illumina HiSeq 2000 paired end sequencing of SAMD00152451 DRX153122 1 1 Illumina TruSeq Stranded mRNA HT Kit   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       1128933600.0 5644668.0 DRR162503 0:100 1:100 A:298341135;C:265514569;G:266315284;T:296956092;N:1806520 100 100     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   Japan 2018-12-24 Adult Adult Heart Cardiovascular System
239 239 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.       heart sample from 7 mpf zebrafish replicate1 SAMD00152450   sample name:h07 1|age:7 month|biological replicate:1|tissue:heart                 Illumina HiSeq 2000 paired end sequencing of SAMD00152450 DRX153121 1 1 Illumina TruSeq Stranded mRNA HT Kit   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       1104589000.0 5522945.0 DRR162502 0:100 1:100 A:296710605;C:254979238;G:256772800;T:294385639;N:1740718 100 100     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   Japan 2018-12-24 Adult Adult Heart Cardiovascular System
8065 8065 ERR035546 ERX013539 ERS017860 ERP000447 PRJEB2368 Sanger zebrafish sequencing E-MTAB-460 Other       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                 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   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   United Kingdom 2011-02-03 Adult Adult Heart Cardiovascular System
8071 8071 ERR023150 ERX009447 ERS017860 ERP000447 PRJEB2368 Sanger zebrafish sequencing E-MTAB-460 Other       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                 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     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   United Kingdom 2011-02-03 Adult Adult Heart Cardiovascular System
8073 8073 ERR023145 ERX009445 ERS017860 ERP000447 PRJEB2368 Sanger zebrafish sequencing E-MTAB-460 Other       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                 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     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   United Kingdom 2011-02-03 Adult Adult Heart Cardiovascular System
11174 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   Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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                 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ba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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   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     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   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11175 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   Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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                 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ba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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   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     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   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11176 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   Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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                 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ba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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   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     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   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11177 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   Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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                 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ba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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   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     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   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11178 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   Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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                 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ba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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   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     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   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11179 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   Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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                 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ba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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   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     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   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11180 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   Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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                 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ba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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   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     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   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11181 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   Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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                 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ba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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   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     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   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11182 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   Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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                 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ba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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   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     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   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11183 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   Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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                 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ba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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   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     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   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11184 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   Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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                 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ba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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   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     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   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11185 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   Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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                 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ba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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   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     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   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11186 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   Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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                 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ba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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   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     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   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11187 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   Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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                 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ba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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   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     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   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11188 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   Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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                 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ba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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   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     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   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11189 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   Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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                 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ba / ; cryabbvu613 crybb / ; 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ba / ; cryabbvu613 crybb / ; 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   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     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   United States 2022-09-24 Adult Adult Heart Cardiovascular System
15017 15017 ERR12352459 ERX11729321 ERS17282126 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Trpc6a KO sham 3 SAMEA114857167 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857167|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Trpc6a KO sham 3|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Trpc6a knockout|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:sham operated|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Trpc6a KO sham 3|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Trpc6a KO sham 3 p Trpc6a KO sham 3 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 3-Trpc6-KO-sham_R1_001.fastq.gz 3-Trpc6-KO-sham_R2_001.fastq.gz fastq fastq 9486677705.0 33558571.0 E MTAB 13603:3 Trpc6 KO sham R 0:141.09 1:141.60 A:2537673665;C:2192877777;G:2224713939;T:2525303945;N:6108379 141 141     2537673665 2192877777 2224713939 2525303945 6108379 ERX11729321 ERS17282126 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.95729 0.95618 0.07289 0.07124 0.7725 0.77481 0.52646 0.53221 149 150 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
15018 15018 ERR12352449 ERX11729311 ERS17282116 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Control 7dpa 1 SAMEA114857157 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857157|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Control 7dpa 1|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:cardiac resection|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Control 7dpa 1|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Control 7dpa 1 p Control 7dpa 1 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 4-Control-7dpa_R2_001.fastq.gz 4-Control-7dpa_R1_001.fastq.gz fastq fastq 6795430724.0 23938740.0 E MTAB 13603:4 Control 7dpa R 0:141.55 1:142.32 A:1815845541;C:1567718020;G:1597570908;T:1808008628;N:6287627 141 142     1815845541 1567718020 1597570908 1808008628 6287627 ERX11729311 ERS17282116 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.94648 0.94563 0.09062 0.08917 0.75087 0.75333 0.52273 0.51959 149 150 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
15019 15019 ERR12352452 ERX11729314 ERS17282119 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Control sham 1 SAMEA114857160 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857160|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Control sham 1|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:sham operated|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Control sham 1|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Control sham 1 p Control sham 1 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 1-Control-sham_R1_001.fastq.gz 1-Control-sham_R2_001.fastq.gz fastq fastq 15636676800.0 52122256.0 E MTAB 13603:1 Control sham R 0:150 1:150 A:4263031098;C:3519985187;G:3706349796;T:4147090133;N:220586 150 150     4263031098 3519985187 3706349796 4147090133 220586 ERX11729314 ERS17282119 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.94648 0.94897 0.06005 0.05942 0.76712 0.76822 0.51256 0.50643 150 150 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
15020 15020 ERR12352451 ERX11729313 ERS17282118 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Control 7dpa 3 SAMEA114857159 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857159|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Control 7dpa 3|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:cardiac resection|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Control 7dpa 3|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Control 7dpa 3 p Control 7dpa 3 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 6-Control-7dpa_R1_001.fastq.gz 6-Control-7dpa_R2_001.fastq.gz fastq fastq 8220300600.0 27401002.0 E MTAB 13603:6 Control 7dpa R 0:150 1:150 A:2242736911;C:1858506669;G:1911004513;T:2207938253;N:114254 150 150     2242736911 1858506669 1911004513 2207938253 114254 ERX11729313 ERS17282118 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.94374 0.94281 0.07308 0.07247 0.74028 0.7418 0.50319 0.50503 150 150 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
15021 15021 ERR12352457 ERX11729319 ERS17282124 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Trpc6a KO sham 1 SAMEA114857165 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857165|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Trpc6a KO sham 1|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Trpc6a knockout|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:sham operated|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Trpc6a KO sham 1|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Trpc6a KO sham 1 p Trpc6a KO sham 1 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 1-Trpc6-KO-sham_R1_001.fastq.gz 1-Trpc6-KO-sham_R2_001.fastq.gz fastq fastq 16463891400.0 54879638.0 E MTAB 13603:1 Trpc6 KO sham R 0:150 1:150 A:4481016793;C:3727761629;G:3905685351;T:4349193797;N:233830 150 150     4481016793 3727761629 3905685351 4349193797 233830 ERX11729319 ERS17282124 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.95234 0.95051 0.05908 0.05789 0.77477 0.77605 0.49876 0.50128 150 150 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
15022 15022 ERR12352458 ERX11729320 ERS17282125 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Trpc6a KO sham 2 SAMEA114857166 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857166|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Trpc6a KO sham 2|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Trpc6a knockout|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:sham operated|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Trpc6a KO sham 2|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Trpc6a KO sham 2 p Trpc6a KO sham 2 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 2-Trpc6-KO-sham_R1_001.fastq.gz 2-Trpc6-KO-sham_R2_001.fastq.gz fastq fastq 10449824700.0 34832749.0 E MTAB 13603:2 Trpc6 KO sham R 0:150 1:150 A:2842222574;C:2368784549;G:2449245548;T:2789428695;N:143334 150 150     2842222574 2368784549 2449245548 2789428695 143334 ERX11729320 ERS17282125 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.9539 0.95284 0.05851 0.05781 0.77425 0.77656 0.50514 0.50462 150 150 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
15023 15023 ERR12352453 ERX11729315 ERS17282120 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Control sham 2 SAMEA114857161 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857161|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Control sham 2|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:sham operated|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Control sham 2|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Control sham 2 p Control sham 2 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 2-Control-sham_R1_001.fastq.gz 2-Control-sham_R2_001.fastq.gz fastq fastq 13714149300.0 45713831.0 E MTAB 13603:2 Control sham R 0:150 1:150 A:3744799859;C:3102314317;G:3246683965;T:3620157056;N:194103 150 150     3744799859 3102314317 3246683965 3620157056 194103 ERX11729315 ERS17282120 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.94672 0.94688 0.05944 0.05917 0.76654 0.76773 0.51792 0.51959 150 150 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
15024 15024 ERR12352450 ERX11729312 ERS17282117 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Control 7dpa 2 SAMEA114857158 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857158|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Control 7dpa 2|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:cardiac resection|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Control 7dpa 2|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Control 7dpa 2 p Control 7dpa 2 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 5-Control-7dpa_R1_001.fastq.gz 5-Control-7dpa_R2_001.fastq.gz fastq fastq 9830629200.0 32768764.0 E MTAB 13603:5 Control 7dpa R 0:150 1:150 A:2655376287;C:2237942590;G:2372252275;T:2564920802;N:137246 150 150     2655376287 2237942590 2372252275 2564920802 137246 ERX11729312 ERS17282117 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.94476 0.94389 0.06625 0.06506 0.74197 0.7441 0.50589 0.50685 150 150 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
15025 15025 ERR12352454 ERX11729316 ERS17282121 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Trpc6a KO 7dpa 1 SAMEA114857162 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857162|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Trpc6a KO 7dpa 1|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Trpc6a knockout|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:cardiac resection|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Trpc6a KO 7dpa 1|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Trpc6a KO 7dpa 1 p Trpc6a KO 7dpa 1 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 4-Trpc6-KO-7dpa_R2_001.fastq.gz 4-Trpc6-KO-7dpa_R1_001.fastq.gz fastq fastq 5379338700.0 17931129.0 E MTAB 13603:4 Trpc6 KO 7dpa R 0:150 1:150 A:1451310854;C:1236467303;G:1283161720;T:1408322640;N:76183 150 150     1451310854 1236467303 1283161720 1408322640 76183 ERX11729316 ERS17282121 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.94369 0.94789 0.06027 0.06036 0.74647 0.74649 0.4767 0.50107 150 150 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
15026 15026 ERR12352455 ERX11729317 ERS17282122 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Trpc6a KO 7dpa 2 SAMEA114857163 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857163|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Trpc6a KO 7dpa 2|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Trpc6a knockout|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:cardiac resection|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Trpc6a KO 7dpa 2|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Trpc6a KO 7dpa 2 p Trpc6a KO 7dpa 2 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 5-Trpc6-KO-7dpa_R2_001.fastq.gz 5-Trpc6-KO-7dpa_R1_001.fastq.gz fastq fastq 14033980200.0 46779934.0 E MTAB 13603:5 Trpc6 KO 7dpa R 0:150 1:150 A:3810908166;C:3197374649;G:3343702230;T:3681798453;N:196702 150 150     3810908166 3197374649 3343702230 3681798453 196702 ERX11729317 ERS17282122 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.94801 0.94661 0.06342 0.06201 0.74834 0.75207 0.50789 0.5027 150 150 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
15027 15027 ERR12352456 ERX11729318 ERS17282123 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Trpc6a KO 7dpa 3 SAMEA114857164 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857164|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Trpc6a KO 7dpa 3|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Trpc6a knockout|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:cardiac resection|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Trpc6a KO 7dpa 3|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Trpc6a KO 7dpa 3 p Trpc6a KO 7dpa 3 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 6-Trpc6-KO-7dpa_R2_001.fastq.gz 6-Trpc6-KO-7dpa_R1_001.fastq.gz fastq fastq 10056041651.0 35562752.0 E MTAB 13603:6 Trpc6 KO 7dpa R 0:141.00 1:141.77 A:2670755890;C:2335065805;G:2381199297;T:2659552078;N:9468581 141 141     2670755890 2335065805 2381199297 2659552078 9468581 ERX11729318 ERS17282123 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.95324 0.9515 0.07632 0.07479 0.75597 0.75787 0.51981 0.52087 113 113 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
30708 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 µM were collected for RNA seq.   pubmed:40053597   DAPT 3 GSM8144970   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 μM to 96 hpf. 1 μg 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 Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h. tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DAPT GSM8144970 GSM8144970: DAPT 3; Danio rerio; RNA Seq GSM8144970 r1 GSM8144970 1 1 μg 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP494974     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     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   China 2024-03-13 Larval Larval Heart Cardiovascular System
30709 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 µM were collected for RNA seq.   pubmed:40053597   DAPT 2 GSM8144969   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 μM to 96 hpf. 1 μg 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 Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h. tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DAPT GSM8144969 GSM8144969: DAPT 2; Danio rerio; RNA Seq GSM8144969 r1 GSM8144969 1 1 μg 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP494974     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     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   China 2024-03-13 Larval Larval Heart Cardiovascular System
30710 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 µM were collected for RNA seq.   pubmed:40053597   DAPT 1 GSM8144968   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 μM to 96 hpf. 1 μg 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 Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h. tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DAPT GSM8144968 GSM8144968: DAPT 1; Danio rerio; RNA Seq GSM8144968 r1 GSM8144968 1 1 μg 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP494974     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     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   China 2024-03-13 Larval Larval Heart Cardiovascular System
30711 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 µM were collected for RNA seq.   pubmed:40053597   DMSO 3 GSM8144967   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 μM to 96 hpf. 1 μg 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 Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h. tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DMSO GSM8144967 GSM8144967: DMSO 3; Danio rerio; RNA Seq GSM8144967 r1 GSM8144967 1 1 μg 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP494974     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     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   China 2024-03-13 Larval Larval Heart Cardiovascular System
30712 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 µM were collected for RNA seq.   pubmed:40053597   DMSO 2 GSM8144966   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 μM to 96 hpf. 1 μg 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 Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h. tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DMSO GSM8144966 GSM8144966: DMSO 2; Danio rerio; RNA Seq GSM8144966 r1 GSM8144966 1 1 μg 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP494974     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     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   China 2024-03-13 Larval Larval Heart Cardiovascular System
30713 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 µM were collected for RNA seq.   pubmed:40053597   DMSO 1 GSM8144965   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 μM to 96 hpf. 1 μg 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 Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h. tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DMSO GSM8144965 GSM8144965: DMSO 1; Danio rerio; RNA Seq GSM8144965 r1 GSM8144965 1 1 μg 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP494974     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     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   China 2024-03-13 Larval Larval Heart Cardiovascular System
31545 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   pubmed:39271818   myd88 3 GSM8163706   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP497581   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     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                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Germany 2024-03-25 Undetermined Undetermined Heart Cardiovascular System
31546 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   pubmed:39271818   myd88 2 GSM8163705   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP497581   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     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                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Germany 2024-03-25 Undetermined Undetermined Heart Cardiovascular System
31547 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   pubmed:39271818   myd88 1 GSM8163704   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP497581   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     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                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Germany 2024-03-25 Undetermined Undetermined Heart Cardiovascular System
31548 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   pubmed:39271818   WT 3 GSM8163703   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP497581   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     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                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Germany 2024-03-25 Undetermined Undetermined Heart Cardiovascular System
31549 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   pubmed:39271818   WT 2 GSM8163702   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP497581   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     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                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Germany 2024-03-25 Undetermined Undetermined Heart Cardiovascular System
31550 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   pubmed:39271818   WT 1 GSM8163701   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP497581   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     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                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Germany 2024-03-25 Undetermined Undetermined Heart Cardiovascular System
31715 31715 SRR28508805 SRX24109965 SRS20897113 SRP498846 PRJNA1094457 Danio rerio Transcriptome or Gene expression PRJNA1094457 Other Atrial cardiomyopathy which often comes with underlying genetic defects has been recognized as a possible substrate of atrial fibrillation. MYH6 encodes a myosin heavy chain a MHC predominantly expressed in the atria and pivotal in sarcomere organization and muscle contraction. However the role of MYH6 in atrial diseases has not been fully elucidated and the genetic cause of atrial cardiomyopathy needs further investigation. Here we employed CRISPR/Cas9 to generate myh6 knockout zebrafish assessing cardiac function through diverse methodologies including video analysis ECG echocardiography transmission electron microscopy and transcriptomic sequencing. Our findings revealed that myh6 defects in zebrafish led to impaired atrial and ventricular function and disordered sarcomere. This research underscores the pivotal role of MYH6 in maintaining atrial function and development. The observed connections between sarcomeric gene variants and atrial cardiomyopathy contribute to our understanding of the genetic basis of atrial fibrillation.       myh6+/ 3 Sample 6   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:6 mpf|dev stage:not collected|collection date:2023 09 03|geo loc name:not collected|sex:pooled male and female|tissue:heart|genotype:myh6+/ |BioSampleModel:Model organism or animal                 myh6+/ 3 Sample 6 Sample 6 Sequencing data were analyzed by R studio Version 2023.03.0+386. Differentially expressed genes DEGs between the experimental myh6+/ and control wildtype groups were identified using the DESeq2 package.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498846     7_230906N_S64_L004_R1_001.fastq.gz 7_230906N_S64_L004_R2_001.fastq.gz fastq fastq 5096818364.0 16876882.0 7 230906N S64 L004 R1 001.fastq.gz 0:151 1:151 A:1417476599;C:1123713516;G:1180970526;T:1374564888;N:92835 151 151     1417476599 1123713516 1180970526 1374564888 92835 SRX24109965 SRS20897113 SRA1836610 Nanjing medical university|Cardiology Nanjing medical university 2 0.92843 0.93025 0.09825 0.0937 0.7601 0.76081 0.46245 0.45548 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-31 Adult Adult Heart Cardiovascular System
31716 31716 SRR28508806 SRX24109964 SRS20897112 SRP498846 PRJNA1094457 Danio rerio Transcriptome or Gene expression PRJNA1094457 Other Atrial cardiomyopathy which often comes with underlying genetic defects has been recognized as a possible substrate of atrial fibrillation. MYH6 encodes a myosin heavy chain a MHC predominantly expressed in the atria and pivotal in sarcomere organization and muscle contraction. However the role of MYH6 in atrial diseases has not been fully elucidated and the genetic cause of atrial cardiomyopathy needs further investigation. Here we employed CRISPR/Cas9 to generate myh6 knockout zebrafish assessing cardiac function through diverse methodologies including video analysis ECG echocardiography transmission electron microscopy and transcriptomic sequencing. Our findings revealed that myh6 defects in zebrafish led to impaired atrial and ventricular function and disordered sarcomere. This research underscores the pivotal role of MYH6 in maintaining atrial function and development. The observed connections between sarcomeric gene variants and atrial cardiomyopathy contribute to our understanding of the genetic basis of atrial fibrillation.       myh6+/ 2 Sample 5   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:6 mpf|dev stage:not collected|collection date:2023 09 03|geo loc name:not collected|sex:pooled male and female|tissue:heart|genotype:myh6+/ |BioSampleModel:Model organism or animal                 myh6+/ 2 Sample 5 Sample 5 Sequencing data were analyzed by R studio Version 2023.03.0+386. Differentially expressed genes DEGs between the experimental myh6+/ and control wildtype groups were identified using the DESeq2 package.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498846     5_230906N_S62_L004_R2_001.fastq.gz 5_230906N_S62_L004_R1_001.fastq.gz fastq fastq 6194790402.0 20512551.0 5 230906N S62 L004 R1 001.fastq.gz 0:151 1:151 A:1714858851;C:1363381540;G:1448185824;T:1668247206;N:116981 151 151     1714858851 1363381540 1448185824 1668247206 116981 SRX24109964 SRS20897112 SRA1836610 Nanjing medical university|Cardiology Nanjing medical university 2 0.93019 0.93196 0.09367 0.08848 0.75444 0.75741 0.48694 0.48749 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-31 Adult Adult Heart Cardiovascular System
31717 31717 SRR28508807 SRX24109963 SRS20897111 SRP498846 PRJNA1094457 Danio rerio Transcriptome or Gene expression PRJNA1094457 Other Atrial cardiomyopathy which often comes with underlying genetic defects has been recognized as a possible substrate of atrial fibrillation. MYH6 encodes a myosin heavy chain a MHC predominantly expressed in the atria and pivotal in sarcomere organization and muscle contraction. However the role of MYH6 in atrial diseases has not been fully elucidated and the genetic cause of atrial cardiomyopathy needs further investigation. Here we employed CRISPR/Cas9 to generate myh6 knockout zebrafish assessing cardiac function through diverse methodologies including video analysis ECG echocardiography transmission electron microscopy and transcriptomic sequencing. Our findings revealed that myh6 defects in zebrafish led to impaired atrial and ventricular function and disordered sarcomere. This research underscores the pivotal role of MYH6 in maintaining atrial function and development. The observed connections between sarcomeric gene variants and atrial cardiomyopathy contribute to our understanding of the genetic basis of atrial fibrillation.       myh6+/ 1 Sample 4   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:6 mpf|dev stage:not collected|collection date:2023 09 03|geo loc name:not collected|sex:pooled male and female|tissue:heart|genotype:myh6+/ |BioSampleModel:Model organism or animal                 myh6+/ 1 Sample 4 Sample 4 Sequencing data were analyzed by R studio Version 2023.03.0+386. Differentially expressed genes DEGs between the experimental myh6+/ and control wildtype groups were identified using the DESeq2 package.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498846     1_230906N_S59_L004_R2_001.fastq.gz 1_230906N_S59_L004_R1_001.fastq.gz fastq fastq 5707073690.0 18897595.0 1 230906N S59 L004 R1 001.fastq.gz 0:151 1:151 A:1590227722;C:1248119772;G:1327453455;T:1541167866;N:104875 151 151     1590227722 1248119772 1327453455 1541167866 104875 SRX24109963 SRS20897111 SRA1836610 Nanjing medical university|Cardiology Nanjing medical university 2 0.92942 0.93069 0.10355 0.09914 0.75745 0.76041 0.48155 0.48754 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-31 Adult Adult Heart Cardiovascular System
31718 31718 SRR28508808 SRX24109962 SRS20897110 SRP498846 PRJNA1094457 Danio rerio Transcriptome or Gene expression PRJNA1094457 Other Atrial cardiomyopathy which often comes with underlying genetic defects has been recognized as a possible substrate of atrial fibrillation. MYH6 encodes a myosin heavy chain a MHC predominantly expressed in the atria and pivotal in sarcomere organization and muscle contraction. However the role of MYH6 in atrial diseases has not been fully elucidated and the genetic cause of atrial cardiomyopathy needs further investigation. Here we employed CRISPR/Cas9 to generate myh6 knockout zebrafish assessing cardiac function through diverse methodologies including video analysis ECG echocardiography transmission electron microscopy and transcriptomic sequencing. Our findings revealed that myh6 defects in zebrafish led to impaired atrial and ventricular function and disordered sarcomere. This research underscores the pivotal role of MYH6 in maintaining atrial function and development. The observed connections between sarcomeric gene variants and atrial cardiomyopathy contribute to our understanding of the genetic basis of atrial fibrillation.       WT 3 Sample 3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:6 mpf|dev stage:not collected|collection date:2023 09 03|geo loc name:not collected|sex:pooled male and female|tissue:heart|genotype:wild type|BioSampleModel:Model organism or animal                 WT 3 Sample 3 Sample 3 Sequencing data were analyzed by R studio Version 2023.03.0+386. Differentially expressed genes DEGs between the experimental myh6+/ and control wildtype groups were identified using the DESeq2 package.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498846     6_230906N_S63_L004_R1_001.fastq.gz 6_230906N_S63_L004_R2_001.fastq.gz fastq fastq 6134248160.0 20312080.0 6 230906N S63 L004 R1 001.fastq.gz 0:151 1:151 A:1703789586;C:1348484209;G:1426369972;T:1655488984;N:115409 151 151     1703789586 1348484209 1426369972 1655488984 115409 SRX24109962 SRS20897110 SRA1836610 Nanjing medical university|Cardiology Nanjing medical university 2 0.92941 0.93008 0.087 0.08333 0.76946 0.77033 0.47664 0.48975 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-31 Adult Adult Heart Cardiovascular System
31719 31719 SRR28508809 SRX24109961 SRS20897109 SRP498846 PRJNA1094457 Danio rerio Transcriptome or Gene expression PRJNA1094457 Other Atrial cardiomyopathy which often comes with underlying genetic defects has been recognized as a possible substrate of atrial fibrillation. MYH6 encodes a myosin heavy chain a MHC predominantly expressed in the atria and pivotal in sarcomere organization and muscle contraction. However the role of MYH6 in atrial diseases has not been fully elucidated and the genetic cause of atrial cardiomyopathy needs further investigation. Here we employed CRISPR/Cas9 to generate myh6 knockout zebrafish assessing cardiac function through diverse methodologies including video analysis ECG echocardiography transmission electron microscopy and transcriptomic sequencing. Our findings revealed that myh6 defects in zebrafish led to impaired atrial and ventricular function and disordered sarcomere. This research underscores the pivotal role of MYH6 in maintaining atrial function and development. The observed connections between sarcomeric gene variants and atrial cardiomyopathy contribute to our understanding of the genetic basis of atrial fibrillation.       WT 2 Sample 2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:6 mpf|dev stage:not collected|collection date:2023 09 03|geo loc name:not collected|sex:pooled male and female|tissue:heart|genotype:wild type|BioSampleModel:Model organism or animal                 WT 2 Sample 2 Sample 2 Sequencing data were analyzed by R studio Version 2023.03.0+386. Differentially expressed genes DEGs between the experimental myh6+/ and control wildtype groups were identified using the DESeq2 package.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498846     4_230906N_S61_L004_R1_001.fastq.gz 4_230906N_S61_L004_R2_001.fastq.gz fastq fastq 6573338342.0 21766021.0 4 230906N S61 L004 R1 001.fastq.gz 0:151 1:151 A:1838220811;C:1442852455;G:1512987676;T:1779153110;N:124290 151 151     1838220811 1442852455 1512987676 1779153110 124290 SRX24109961 SRS20897109 SRA1836610 Nanjing medical university|Cardiology Nanjing medical university 2 0.9373 0.93754 0.08495 0.07972 0.7766 0.77897 0.48726 0.50532 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-31 Adult Adult Heart Cardiovascular System
31720 31720 SRR28508810 SRX24109960 SRS20897108 SRP498846 PRJNA1094457 Danio rerio Transcriptome or Gene expression PRJNA1094457 Other Atrial cardiomyopathy which often comes with underlying genetic defects has been recognized as a possible substrate of atrial fibrillation. MYH6 encodes a myosin heavy chain a MHC predominantly expressed in the atria and pivotal in sarcomere organization and muscle contraction. However the role of MYH6 in atrial diseases has not been fully elucidated and the genetic cause of atrial cardiomyopathy needs further investigation. Here we employed CRISPR/Cas9 to generate myh6 knockout zebrafish assessing cardiac function through diverse methodologies including video analysis ECG echocardiography transmission electron microscopy and transcriptomic sequencing. Our findings revealed that myh6 defects in zebrafish led to impaired atrial and ventricular function and disordered sarcomere. This research underscores the pivotal role of MYH6 in maintaining atrial function and development. The observed connections between sarcomeric gene variants and atrial cardiomyopathy contribute to our understanding of the genetic basis of atrial fibrillation.       WT 1 Sample 1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:6 mpf|dev stage:not collected|collection date:2023 09 03|geo loc name:not collected|sex:pooled male and female|tissue:heart|genotype:wild type|BioSampleModel:Model organism or animal                 WT 1 Sample 1 Sample 1 Sequencing data were analyzed by R studio Version 2023.03.0+386. Differentially expressed genes DEGs between the experimental myh6+/ and control wildtype groups were identified using the DESeq2 package.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498846     3_230906N_S1_L004_R2_001.fastq.gz 3_230906N_S1_L004_R1_001.fastq.gz fastq fastq 6962707546.0 23055323.0 3 230906N S1 L004 R1 001.fastq.gz 0:151 1:151 A:1938531865;C:1527591368;G:1608823948;T:1887630666;N:129699 151 151     1938531865 1527591368 1608823948 1887630666 129699 SRX24109960 SRS20897108 SRA1836610 Nanjing medical university|Cardiology Nanjing medical university 2 0.84836 0.93866 0.08283 0.08602 0.7696 0.764 0.48014 0.48678 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-31 Adult Adult Heart Cardiovascular System
31994 31994 SRR28906400 SRX24462857 SRS21215803 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H KO 1dpt 1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.45 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H KO 1dpt 1 H KO 1dpt 1 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-KO-1dpt-1_2.fq.gz H-KO-1dpt-1_1.fq.gz fastq fastq 7562116200.0 25207054.0 H KO 1dpt 1 1.fq.gz 0:150 1:150 A:2053051017;C:1729576392;G:1752482225;T:2025170234;N:1836332 150 150     2053051017 1729576392 1752482225 2025170234 1836332 SRX24462857 SRS21215803 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.94384 0.94341 0.0998 0.09865 0.71433 0.71427 0.49335 0.49672 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
31995 31995 SRR28906401 SRX24462856 SRS21215806 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H WT 1dpt 3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.44 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H WT 1dpt 3 H WT 1dpt 3 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-WT-1dpt-3_1.fq.gz H-WT-1dpt-3_2.fq.gz fastq fastq 7976703000.0 26589010.0 H WT 1dpt 3 1.fq.gz 0:150 1:150 A:2168595183;C:1821923593;G:1848475154;T:2135714236;N:1994834 150 150     2168595183 1821923593 1848475154 2135714236 1994834 SRX24462856 SRS21215806 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.94335 0.9438 0.10093 0.10044 0.7122 0.71031 0.50824 0.51139 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
31996 31996 SRR28906402 SRX24462855 SRS21215805 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H WT 1dpt 2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.43 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H WT 1dpt 2 H WT 1dpt 2 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-WT-1dpt-2_2.fq.gz H-WT-1dpt-2_1.fq.gz fastq fastq 7656200400.0 25520668.0 H WT 1dpt 2 1.fq.gz 0:150 1:150 A:2082823123;C:1745563595;G:1770285873;T:2055608172;N:1919637 150 150     2082823123 1745563595 1770285873 2055608172 1919637 SRX24462855 SRS21215805 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.9435 0.94385 0.1003 0.10068 0.71015 0.70956 0.51199 0.51323 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
31997 31997 SRR28906403 SRX24462854 SRS21215800 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H WT 1dpt 1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.42 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H WT 1dpt 1 H WT 1dpt 1 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-WT-1dpt-1_1.fq.gz H-WT-1dpt-1_2.fq.gz fastq fastq 7762317300.0 25874391.0 H WT 1dpt 1 1.fq.gz 0:150 1:150 A:2110489933;C:1771640570;G:1794995113;T:2083336499;N:1855185 150 150     2110489933 1771640570 1794995113 2083336499 1855185 SRX24462854 SRS21215800 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.94438 0.94341 0.0996 0.09862 0.70989 0.70952 0.51628 0.50961 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
31998 31998 SRR28906404 SRX24462853 SRS21215801 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H KO UI 3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.41 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H KO UI 3 H KO UI 3 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-KO-UI-3_1.fq.gz H-KO-UI-3_2.fq.gz fastq fastq 8074894200.0 26916314.0 H KO UI 3 1.fq.gz 0:150 1:150 A:2188747586;C:1844507036;G:1872467804;T:2167174432;N:1997342 150 150     2188747586 1844507036 1872467804 2167174432 1997342 SRX24462853 SRS21215801 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.94616 0.9458 0.08568 0.08577 0.72163 0.72127 0.49125 0.49327 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
31999 31999 SRR28906405 SRX24462852 SRS21215802 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H KO UI 2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.40 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H KO UI 2 H KO UI 2 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-KO-UI-2_1.fq.gz H-KO-UI-2_2.fq.gz fastq fastq 7322976300.0 24409921.0 H KO UI 2 1.fq.gz 0:150 1:150 A:1977575170;C:1682113004;G:1705811265;T:1955632804;N:1844057 150 150     1977575170 1682113004 1705811265 1955632804 1844057 SRX24462852 SRS21215802 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.94609 0.94626 0.08289 0.08343 0.72251 0.72206 0.47771 0.48416 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
32000 32000 SRR28906406 SRX24462851 SRS21215799 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H KO UI 1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.39 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H KO UI 1 H KO UI 1 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-KO-UI-1_1.fq.gz H-KO-UI-1_2.fq.gz fastq fastq 7719372900.0 25731243.0 H KO UI 1 1.fq.gz 0:150 1:150 A:2090530132;C:1765932073;G:1794848389;T:2066130430;N:1931876 150 150     2090530132 1765932073 1794848389 2066130430 1931876 SRX24462851 SRS21215799 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.94579 0.94669 0.08477 0.08495 0.72224 0.72149 0.47982 0.48098 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
32001 32001 SRR28906407 SRX24462850 SRS21215798 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H KO 7dpt 3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.59 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H KO 7dpt 3 H KO 7dpt 3 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-KO-7dpt-3_1.fq.gz H-KO-7dpt-3_2.fq.gz fastq fastq 8751619200.0 29172064.0 H KO 7dpt 3 1.fq.gz 0:150 1:150 A:2378357776;C:1995299013;G:2022275849;T:2353549435;N:2137127 150 150     2378357776 1995299013 2022275849 2353549435 2137127 SRX24462850 SRS21215798 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.94284 0.94237 0.10245 0.10267 0.71534 0.71522 0.48671 0.48061 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
32002 32002 SRR28906408 SRX24462849 SRS21215797 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H KO 7dpt 2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.58 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H KO 7dpt 2 H KO 7dpt 2 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-KO-7dpt-2_2.fq.gz H-KO-7dpt-2_1.fq.gz fastq fastq 8704213200.0 29014044.0 H KO 7dpt 2 1.fq.gz 0:150 1:150 A:2361470638;C:1987488058;G:2014448011;T:2338898652;N:1907841 150 150     2361470638 1987488058 2014448011 2338898652 1907841 SRX24462849 SRS21215797 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.94331 0.94387 0.10094 0.10045 0.71536 0.71356 0.48579 0.48959 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
32003 32003 SRR28906409 SRX24462848 SRS21215793 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H KO 7dpt 1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.57 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H KO 7dpt 1 H KO 7dpt 1 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-KO-7dpt-1_1.fq.gz H-KO-7dpt-1_2.fq.gz fastq fastq 8217376500.0 27391255.0 H KO 7dpt 1 1.fq.gz 0:150 1:150 A:2225497058;C:1878586733;G:1906220197;T:2205098635;N:1973877 150 150     2225497058 1878586733 1906220197 2205098635 1973877 SRX24462848 SRS21215793 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.94328 0.94383 0.10058 0.10047 0.71256 0.71141 0.47543 0.4729 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
32004 32004 SRR28906410 SRX24462847 SRS21215792 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H WT 7dpt 3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.56 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H WT 7dpt 3 H WT 7dpt 3 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-WT-7dpt-3_1.fq.gz H-WT-7dpt-3_2.fq.gz fastq fastq 8481387900.0 28271293.0 H WT 7dpt 3 1.fq.gz 0:150 1:150 A:2299162401;C:1934779265;G:1965090511;T:2280371695;N:1984028 150 150     2299162401 1934779265 1965090511 2280371695 1984028 SRX24462847 SRS21215792 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.94277 0.94304 0.1044 0.10406 0.71912 0.71916 0.48211 0.48332 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
32005 32005 SRR28906411 SRX24462846 SRS21215794 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H WT UI 3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.38 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H WT UI 3 H WT UI 3 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-WT-UI-3_1.fq.gz H-WT-UI-3_2.fq.gz fastq fastq 7688910600.0 25629702.0 H WT UI 3 1.fq.gz 0:150 1:150 A:2097391352;C:1749410635;G:1772959080;T:2067249011;N:1900522 150 150     2097391352 1749410635 1772959080 2067249011 1900522 SRX24462846 SRS21215794 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.94913 0.94883 0.08493 0.08488 0.74391 0.74412 0.49665 0.49102 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
32006 32006 SRR28906412 SRX24462845 SRS21215789 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H WT 7dpt 2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.55 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H WT 7dpt 2 H WT 7dpt 2 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-WT-7dpt-2_1.fq.gz H-WT-7dpt-2_2.fq.gz fastq fastq 8122767900.0 27075893.0 H WT 7dpt 2 1.fq.gz 0:150 1:150 A:2209122325;C:1845876653;G:1874400213;T:2191385562;N:1983147 150 150     2209122325 1845876653 1874400213 2191385562 1983147 SRX24462845 SRS21215789 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.94213 0.94221 0.1066 0.10643 0.72143 0.72054 0.47732 0.47973 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
32007 32007 SRR28906413 SRX24462844 SRS21215795 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H WT 7dpt 1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.54 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H WT 7dpt 1 H WT 7dpt 1 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-WT-7dpt-1_1.fq.gz H-WT-7dpt-1_2.fq.gz fastq fastq 8528784300.0 28429281.0 H WT 7dpt 1 1.fq.gz 0:150 1:150 A:2315405815;C:1946703478;G:1973240605;T:2291355768;N:2078634 150 150     2315405815 1946703478 1973240605 2291355768 2078634 SRX24462844 SRS21215795 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.94286 0.94346 0.10556 0.10568 0.72129 0.72038 0.48324 0.48088 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
32008 32008 SRR28906414 SRX24462843 SRS21215796 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H KO 3dpt 3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.53 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H KO 3dpt 3 H KO 3dpt 3 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-KO-3dpt-3_1.fq.gz H-KO-3dpt-3_2.fq.gz fastq fastq 8342832900.0 27809443.0 H KO 3dpt 3 1.fq.gz 0:150 1:150 A:2266689673;C:1905685494;G:1930305329;T:2238163657;N:1988747 150 150     2266689673 1905685494 1930305329 2238163657 1988747 SRX24462843 SRS21215796 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.94595 0.94499 0.09639 0.09628 0.715 0.71553 0.49016 0.49123 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
32009 32009 SRR28906415 SRX24462842 SRS21215791 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H KO 3dpt 2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.52 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H KO 3dpt 2 H KO 3dpt 2 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-KO-3dpt-2_1.fq.gz H-KO-3dpt-2_2.fq.gz fastq fastq 7442766300.0 24809221.0 H KO 3dpt 2 1.fq.gz 0:150 1:150 A:2019309536;C:1702177984;G:1726456407;T:1993008040;N:1814333 150 150     2019309536 1702177984 1726456407 1993008040 1814333 SRX24462842 SRS21215791 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.94586 0.94468 0.09614 0.09561 0.71648 0.71705 0.49676 0.49381 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
32010 32010 SRR28906416 SRX24462841 SRS21215788 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H KO 3dpt 1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.51 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H KO 3dpt 1 H KO 3dpt 1 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-KO-3dpt-1_1.fq.gz H-KO-3dpt-1_2.fq.gz fastq fastq 7831293600.0 26104312.0 H KO 3dpt 1 1.fq.gz 0:150 1:150 A:2128253770;C:1787608569;G:1811254103;T:2102258260;N:1918898 150 150     2128253770 1787608569 1811254103 2102258260 1918898 SRX24462841 SRS21215788 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.94613 0.94565 0.09774 0.09695 0.71474 0.71474 0.47983 0.47889 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
32011 32011 SRR28906417 SRX24462840 SRS21215790 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H WT 3dpt 3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.50 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H WT 3dpt 3 H WT 3dpt 3 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-WT-3dpt-3_1.fq.gz H-WT-3dpt-3_2.fq.gz fastq fastq 8069992500.0 26899975.0 H WT 3dpt 3 1.fq.gz 0:150 1:150 A:2190393002;C:1843546509;G:1866938814;T:2167244861;N:1869314 150 150     2190393002 1843546509 1866938814 2167244861 1869314 SRX24462840 SRS21215790 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.9433 0.94216 0.09862 0.09804 0.70845 0.70843 0.48894 0.48921 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
32012 32012 SRR28906418 SRX24462839 SRS21215786 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H WT 3dpt 2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.49 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H WT 3dpt 2 H WT 3dpt 2 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-WT-3dpt-2_1.fq.gz H-WT-3dpt-2_2.fq.gz fastq fastq 7502274600.0 25007582.0 H WT 3dpt 2 1.fq.gz 0:150 1:150 A:2036169286;C:1712256370;G:1737197102;T:2014865457;N:1786385 150 150     2036169286 1712256370 1737197102 2014865457 1786385 SRX24462839 SRS21215786 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.94174 0.94129 0.09992 0.09885 0.70865 0.70863 0.48713 0.48657 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
32013 32013 SRR28906419 SRX24462838 SRS21215787 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H WT 3dpt 1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.48 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H WT 3dpt 1 H WT 3dpt 1 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-WT-3dpt-1_1.fq.gz H-WT-3dpt-1_2.fq.gz fastq fastq 7511851800.0 25039506.0 H WT 3dpt 1 1.fq.gz 0:150 1:150 A:2035709532;C:1717586093;G:1742606776;T:2014155061;N:1794338 150 150     2035709532 1717586093 1742606776 2014155061 1794338 SRX24462838 SRS21215787 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.94269 0.9423 0.0996 0.09902 0.70952 0.70978 0.48839 0.48674 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
32014 32014 SRR28906420 SRX24462837 SRS21215785 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H KO 1dpt 3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.47 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H KO 1dpt 3 H KO 1dpt 3 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-KO-1dpt-3_1.fq.gz H-KO-1dpt-3_2.fq.gz fastq fastq 7530376500.0 25101255.0 H KO 1dpt 3 1.fq.gz 0:150 1:150 A:2038997159;C:1723582025;G:1752027912;T:2013934872;N:1834532 150 150     2038997159 1723582025 1752027912 2013934872 1834532 SRX24462837 SRS21215785 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.94529 0.94377 0.09755 0.09638 0.71368 0.71386 0.49782 0.49531 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
32015 32015 SRR28906421 SRX24462836 SRS21215783 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H KO 1dpt 2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.46 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H KO 1dpt 2 H KO 1dpt 2 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-KO-1dpt-2_1.fq.gz H-KO-1dpt-2_2.fq.gz fastq fastq 8198157000.0 27327190.0 H KO 1dpt 2 1.fq.gz 0:150 1:150 A:2235208758;C:1865834372;G:1891495548;T:2203633727;N:1984595 150 150     2235208758 1865834372 1891495548 2203633727 1984595 SRX24462836 SRS21215783 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.9434 0.94233 0.10137 0.10074 0.71516 0.71553 0.48646 0.50212 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
32016 32016 SRR28906422 SRX24462835 SRS21215784 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H WT UI 2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.37 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H WT UI 2 H WT UI 2 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-WT-UI-2_1.fq.gz H-WT-UI-2_2.fq.gz fastq fastq 7635626400.0 25452088.0 H WT UI 2 1.fq.gz 0:150 1:150 A:2078918390;C:1742748243;G:1764521851;T:2047527957;N:1909959 150 150     2078918390 1742748243 1764521851 2047527957 1909959 SRX24462835 SRS21215784 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.94963 0.95039 0.08529 0.08474 0.74432 0.74259 0.48965 0.49738 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
32017 32017 SRR28906423 SRX24462834 SRS21215782 SRP505889 PRJNA1108009 Danio rerio Raw sequence reads PRJNA1108009 Whole Genome Sequencing cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome         H WT UI 1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:3mpf|dev stage:Adult|collection date:2023 08|geo loc name:China:wuhan|sex:male|tissue:heart|lat lon:30.56 N 114.36 E|BioSampleModel:Model organism or animal                 RNA seq of danio rario:adult male heart H WT UI 1 H WT UI 1 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP505889     H-WT-UI-1_1.fq.gz H-WT-UI-1_2.fq.gz fastq fastq 8207182200.0 27357274.0 H WT UI 1 1.fq.gz 0:150 1:150 A:2240283347;C:1864261040;G:1888322709;T:2212265411;N:2049693 150 150     2240283347 1864261040 1888322709 2212265411 2049693 SRX24462834 SRS21215782 SRA1859838 Wuhan University|Taikang Medical School (School of Basic Medical Sc Wuhan University 2 0.94887 0.94936 0.08453 0.08421 0.74298 0.7428 0.50188 0.50215 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-06 Adult Adult Heart Cardiovascular System
32629 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.       tg3 GSM8325761   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   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   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP513565     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     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   United States 2024-06-12 Adult Adult Heart Cardiovascular System
32630 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.       tg2 GSM8325760   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   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   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. Illumina with a 50 bp paired end sequencing protocol in the Mayo Clinic DNA Sequencing Core Facility   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP513565     tgTFEB-2.FCC83VDACXX_L2_R1_ITTAGGC.fastq.gz tgTFEB-2.FCC83VDACXX_L2_R2_ITTAGGC.fastq.gz fastq fastq 5242666176.0 51398688.0 GSM8325760 r1 0:51 1:51 A:1383019833;C:1250736207;G:1222950385;T:1385150031;N:809720 51 51     1383019833 1250736207 1222950385 1385150031 809720 SRX24896628 SRS21602921 SRA1897306 University of Maryland University of Maryland 2 0.93633 0.93686 0.07262 0.07347 0.76386 0.76784 0.50012 0.49374 51 51 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   United States 2024-06-12 Adult Adult Heart Cardiovascular System
32631 32631 SRR29382475 SRX24896627 SRS21602927 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.       tg1 GSM8325759   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   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   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. Illumina with a 50 bp paired end sequencing protocol in the Mayo Clinic DNA Sequencing Core Facility   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP513565     tgTFEB-1.FCC83VDACXX_L2_R1_IATCACG.fastq.gz tgTFEB-1.FCC83VDACXX_L2_R2_IATCACG.fastq.gz fastq fastq 5320541850.0 52162175.0 GSM8325759 r1 0:51 1:51 A:1400067505;C:1273185406;G:1243780050;T:1402679178;N:829711 51 51     1400067505 1273185406 1243780050 1402679178 829711 SRX24896627 SRS21602927 SRA1897306 University of Maryland University of Maryland 2 0.93615 0.93588 0.07079 0.07138 0.76053 0.76501 0.48551 0.49329 51 51 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   United States 2024-06-12 Adult Adult Heart Cardiovascular System
32632 32632 SRR29382476 SRX24896626 SRS21602925 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.       mtor3 GSM8325758   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   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   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP513565     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     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   United States 2024-06-12 Adult Adult Heart Cardiovascular System
32633 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.       mtor2 GSM8325757   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   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   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. Illumina with a 50 bp paired end sequencing protocol in the Mayo Clinic DNA Sequencing Core Facility   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP513565     mTOR_het-2.FCC83VDACXX_L1_R1_IACTGAT.fastq.gz mTOR_het-2.FCC83VDACXX_L1_R2_IACTGAT.fastq.gz fastq fastq 5483398518.0 53758809.0 GSM8325757 r1 0:51 1:51 A:1453287917;C:1302789730;G:1270038475;T:1456290761;N:991635 51 51     1453287917 1302789730 1270038475 1456290761 991635 SRX24896625 SRS21602924 SRA1897306 University of Maryland University of Maryland 2 0.94026 0.93969 0.06999 0.07018 0.77461 0.77747 0.47613 0.47098 51 51 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   United States 2024-06-12 Adult Adult Heart Cardiovascular System
32634 32634 SRR29382478 SRX24896624 SRS21602922 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.       mtor1 GSM8325756   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   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   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. Illumina with a 50 bp paired end sequencing protocol in the Mayo Clinic DNA Sequencing Core Facility   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP513565     mTOR_het-1.FCC83VDACXX_L1_R1_IGAGTGG.fastq.gz mTOR_het-1.FCC83VDACXX_L1_R2_IGAGTGG.fastq.gz fastq fastq 4455003204.0 43676502.0 GSM8325756 r1 0:51 1:51 A:1161215955;C:1076287934;G:1053346373;T:1163349099;N:803843 51 51     1161215955 1076287934 1053346373 1163349099 803843 SRX24896624 SRS21602922 SRA1897306 University of Maryland University of Maryland 2 0.94192 0.94259 0.06914 0.06985 0.77189 0.77376 0.46843 0.47795 51 51 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   United States 2024-06-12 Adult Adult Heart Cardiovascular System
32635 32635 SRR29382479 SRX24896623 SRS21602923 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.       WT3 GSM8325755   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   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   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. Illumina with a 50 bp paired end sequencing protocol in the Mayo Clinic DNA Sequencing Core Facility   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP513565     WT_9M-3.FCC83VDACXX_L1_R1_ICGTACG.fastq.gz WT_9M-3.FCC83VDACXX_L1_R2_ICGTACG.fastq.gz fastq fastq 4538425332.0 44494366.0 GSM8325755 r1 0:51 1:51 A:1204281121;C:1078176760;G:1048311225;T:1206831380;N:824846 51 51     1204281121 1078176760 1048311225 1206831380 824846 SRX24896623 SRS21602923 SRA1897306 University of Maryland University of Maryland 2 0.93601 0.93501 0.07636 0.07669 0.76802 0.7712 0.48936 0.48242 51 51 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   United States 2024-06-12 Adult Adult Heart Cardiovascular System
32636 32636 SRR29382480 SRX24896622 SRS21602920 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.       WT2 GSM8325754   source name:Heart|tissue:Heart|genotype:WT|geo loc name:missing|collection date:missing WT2 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   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   tissue:Heart|genotype:WT GSM8325754 GSM8325754: WT2; Danio rerio; RNA Seq GSM8325754 r1 GSM8325754 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP513565     WT_9M-2.FCC83VDACXX_L1_R1_IGTTTCG.fastq.gz WT_9M-2.FCC83VDACXX_L1_R2_IGTTTCG.fastq.gz fastq fastq 4394783118.0 43086109.0 GSM8325754 r1 0:51 1:51 A:1166430614;C:1043314839;G:1013761771;T:1170479766;N:796128 51 51     1166430614 1043314839 1013761771 1170479766 796128 SRX24896622 SRS21602920 SRA1897306 University of Maryland University of Maryland 2 0.93781 0.93932 0.07533 0.07609 0.7725 0.77415 0.48641 0.49111 51 51 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   United States 2024-06-12 Adult Adult Heart Cardiovascular System
32637 32637 SRR29382481 SRX24896621 SRS21602919 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.       WT1 GSM8325753   source name:Heart|tissue:Heart|genotype:WT|geo loc name:missing|collection date:missing WT1 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   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   tissue:Heart|genotype:WT GSM8325753 GSM8325753: WT1; Danio rerio; RNA Seq GSM8325753 r1 GSM8325753 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP513565     WT_9M-1.FCC83VDACXX_L1_R1_IGTGGCC.fastq.gz WT_9M-1.FCC83VDACXX_L1_R2_IGTGGCC.fastq.gz fastq fastq 4957112586.0 48599143.0 GSM8325753 r1 0:51 1:51 A:1315023360;C:1175864052;G:1150478100;T:1314860199;N:886875 51 51     1315023360 1175864052 1150478100 1314860199 886875 SRX24896621 SRS21602919 SRA1897306 University of Maryland University of Maryland 2 0.93655 0.9382 0.07219 0.0729 0.77595 0.77893 0.45892 0.468 51 51 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   United States 2024-06-12 Adult Adult Heart Cardiovascular System
33609 33609 SRR30247666 SRX25709110 SRS22350227 SRP526520 PRJNA1148340 RNA Seq analyses of hey2 mutant and wild type sibling zebrafish hearts PRJNA1148340 Other To assess the effects of Hey2 deficiency we performed transcriptome analyses of hey2 mutant and wild type sibling zebrafish hearts at 3 mpf.       RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf rep3 KO3   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:OE replicate 3|BioSampleModel:Model organism or animal                 RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf rep3 hey25nt / replicate 3 hey25nt / replicate 3 RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf replicate 3     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP526520     KO_3_1.fq.gz KO_3_2.fq.gz fastq fastq 6793426200.0 22644754.0 KO 3 1.fq.gz 0:150 1:150 A:1845779030;C:1550159613;G:1539592354;T:1857860950;N:34253 150 150     1845779030 1550159613 1539592354 1857860950 34253 SRX25709110 SRS22350227 SRA1948261 East China Normal University|School of Life Sciences East China Normal University 2 0.94555 0.92523 0.0631 0.06139 0.76672 0.76968 0.56501 0.57019 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2024-08-15 Adult Adult Heart Cardiovascular System
33610 33610 SRR30247667 SRX25709109 SRS22350226 SRP526520 PRJNA1148340 RNA Seq analyses of hey2 mutant and wild type sibling zebrafish hearts PRJNA1148340 Other To assess the effects of Hey2 deficiency we performed transcriptome analyses of hey2 mutant and wild type sibling zebrafish hearts at 3 mpf.       RNA Seq for hey25nt / mutantzebrafish hearts at 3 mpf rep2 KO2   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:OE replicate 2|BioSampleModel:Model organism or animal                 RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf rep2 hey25nt / replicate 2 hey25nt / replicate 2 RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf replicate 2     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP526520     KO_2_1.fq.gz KO_2_2.fq.gz fastq fastq 6577703400.0 21925678.0 KO 2 1.fq.gz 0:150 1:150 A:1795319867;C:1492750718;G:1485718638;T:1803881133;N:33044 150 150     1795319867 1492750718 1485718638 1803881133 33044 SRX25709109 SRS22350226 SRA1948261 East China Normal University|School of Life Sciences East China Normal University 2 0.94565 0.92404 0.06212 0.06008 0.77281 0.77546 0.55478 0.56589 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2024-08-15 Adult Adult Heart Cardiovascular System
33611 33611 SRR30247668 SRX25709108 SRS22350225 SRP526520 PRJNA1148340 RNA Seq analyses of hey2 mutant and wild type sibling zebrafish hearts PRJNA1148340 Other To assess the effects of Hey2 deficiency we performed transcriptome analyses of hey2 mutant and wild type sibling zebrafish hearts at 3 mpf.       RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf rep1 KO1   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:OE replicate 1|BioSampleModel:Model organism or animal                 RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf rep1 hey25nt / replicate 1 hey25nt / replicate 1 RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf replicate 1     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP526520     KO_1_2.fq.gz KO_1_1.fq.gz fastq fastq 6592159500.0 21973865.0 KO 1 1.fq.gz 0:150 1:150 A:1800707634;C:1491918482;G:1484850929;T:1814648405;N:34050 150 150     1800707634 1491918482 1484850929 1814648405 34050 SRX25709108 SRS22350225 SRA1948261 East China Normal University|School of Life Sciences East China Normal University 2 0.94443 0.92689 0.06601 0.06488 0.76883 0.77033 0.58332 0.52175 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2024-08-15 Adult Adult Heart Cardiovascular System
33612 33612 SRR30247669 SRX25709107 SRS22350224 SRP526520 PRJNA1148340 RNA Seq analyses of hey2 mutant and wild type sibling zebrafish hearts PRJNA1148340 Other To assess the effects of Hey2 deficiency we performed transcriptome analyses of hey2 mutant and wild type sibling zebrafish hearts at 3 mpf.       RNA Seq for hey2+/+ zebrafish hearts at 3 mpf rep3 WT3   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:CTL replicate 3|BioSampleModel:Model organism or animal                 RNA Seq for hey2+/+ zebrafish hearts at 3 mpf rep3 hey2+/+ replicate 3 hey2+/+ replicate 3 RNA Seq for hey2+/+ zebrafish hearts at 3 mpf replicate 3     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP526520     WT_3_1.fq.gz WT_3_2.fq.gz fastq fastq 6582842700.0 21942809.0 WT 3 1.fq.gz 0:150 1:150 A:1796301568;C:1494922823;G:1487154319;T:1804427831;N:36159 150 150     1796301568 1494922823 1487154319 1804427831 36159 SRX25709107 SRS22350224 SRA1948261 East China Normal University|School of Life Sciences East China Normal University 2 0.94446 0.92023 0.06492 0.06289 0.76694 0.7699 0.55651 0.53407 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2024-08-15 Adult Adult Heart Cardiovascular System
33613 33613 SRR30247670 SRX25709106 SRS22350223 SRP526520 PRJNA1148340 RNA Seq analyses of hey2 mutant and wild type sibling zebrafish hearts PRJNA1148340 Other To assess the effects of Hey2 deficiency we performed transcriptome analyses of hey2 mutant and wild type sibling zebrafish hearts at 3 mpf.       RNA Seq for hey2+/+ zebrafish hearts at 3 mpf rep2 WT2   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:CTL replicate 2|BioSampleModel:Model organism or animal                 RNA Seq for hey2+/+ zebrafish hearts at 3 mpf rep2 hey2+/+ replicate 2 hey2+/+ replicate 2 RNA Seq for hey2+/+ zebrafish hearts at 3 mpf replicate 2     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP526520     WT_2_2.fq.gz WT_2_1.fq.gz fastq fastq 6632526000.0 22108420.0 WT 2 1.fq.gz 0:150 1:150 A:1811392253;C:1505075703;G:1495091968;T:1820928778;N:37298 150 150     1811392253 1505075703 1495091968 1820928778 37298 SRX25709106 SRS22350223 SRA1948261 East China Normal University|School of Life Sciences East China Normal University 2 0.94532 0.92096 0.06496 0.06227 0.76564 0.76909 0.56754 0.57117 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2024-08-15 Adult Adult Heart Cardiovascular System

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