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1,351 rows where experiment.platform = "ILLUMINA", technology = "unknown" and tissue_curation_coarse = "Cardiovascular System"

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experiment.library_selection 10

devstage_curation 8

devstage_curation_coarse 6

tissue_curation 3

experiment.library_strategy 3

experiment.library_layout 2

tissue_curation_coarse 1

  • Cardiovascular System · 1,351 ✖

technology 1

  • unknown · 1,351 ✖

experiment.platform 1

  • ILLUMINA · 1,351 ✖

experiment.library_source 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
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
5879 5879 ERR1759701 ERX1826022 ERS1474296 ERP020578 PRJEB18632 RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf E-MTAB-5323 Transcriptome Analysis The aim of this analysis is to uncover novel molecules synthesized and secreted from cardiomyocytes. ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323   Protocols: To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs. Sample2 SAMEA27136168 Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27136168|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample2|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:actn2 tdEodncv44Tg|sample name:E MTAB 5323:Sample2                 Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf E MTAB 5323:Sample2 s Sample2 s RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture’s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs. Experimental Factor: Tgmyl7:actn2 tdEodncv44Tg:genotype RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiSeq   ERP020578 Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16 mochizukis_lab_myl7_actn2tdEos_72h_01.fastq.gz fastq 448234901.0 6016977.0 E MTAB 5323:Sample2 0:74.50 1:0 A:118923409;C:100586009;G:99987046;T:126071553;N:2666884 74 0     118923409 100586009 99987046 126071553 2666884 ERX1826022 ERS1474296 ERA776061 Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive 1 0.88465   0.27583   0.75398   0.55917   75   B   usable mapping rate illumina miseq full_length poly_a nebnext bulk unknown unknown   Japan 2016-12-15 Larval Larval Heart Cardiovascular System
5880 5880 ERR1759702 ERX1826022 ERS1474296 ERP020578 PRJEB18632 RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf E-MTAB-5323 Transcriptome Analysis The aim of this analysis is to uncover novel molecules synthesized and secreted from cardiomyocytes. ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323   Protocols: To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs. Sample2 SAMEA27136168 Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27136168|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample2|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:actn2 tdEodncv44Tg|sample name:E MTAB 5323:Sample2                 Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf E MTAB 5323:Sample2 s Sample2 s RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture’s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs. Experimental Factor: Tgmyl7:actn2 tdEodncv44Tg:genotype RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiSeq   ERP020578 Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16 mochizukis_lab_myl7_actn2tdEos_72h_02.fastq.gz fastq 448116860.0 6016977.0 E MTAB 5323:Sample2 1 0:0 1:74.48 A:127811460;C:99875207;G:106561979;T:113792335;N:75879 0 74     127811460 99875207 106561979 113792335 75879 ERX1826022 ERS1474296 ERA776061 Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive 1 0.91589   0.2509   0.79005   0.54852   75   B   usable mapping rate illumina miseq full_length poly_a nebnext bulk unknown unknown   Japan 2016-12-15 Larval Larval Heart Cardiovascular System
5881 5881 ERR1759699 ERX1826021 ERS1474295 ERP020578 PRJEB18632 RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf E-MTAB-5323 Transcriptome Analysis The aim of this analysis is to uncover novel molecules synthesized and secreted from cardiomyocytes. ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323   Protocols: To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs. Sample1 SAMEA27135418 Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27135418|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample1|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:Nls mCherryncv11Tg|sample name:E MTAB 5323:Sample1                 Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf E MTAB 5323:Sample1 s Sample1 s RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture’s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs. Experimental Factor: Tgmyl7:Nls mCherryncv11Tg:genotype RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiSeq   ERP020578 Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16 mochizukis_lab_myl7_NLSmCherry_72h_01.fastq.gz fastq 766363334.0 10284347.0 E MTAB 5323:Sample1 0:74.52 1:0 A:201960096;C:174999154;G:173403690;T:211341998;N:4658396 74 0     201960096 174999154 173403690 211341998 4658396 ERX1826021 ERS1474295 ERA776061 Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive 1 0.86003   0.20554   0.76301   0.55753   74   B   usable mapping rate illumina miseq full_length poly_a nebnext bulk unknown unknown   Japan 2016-12-15 Larval Larval Heart Cardiovascular System
5882 5882 ERR1759700 ERX1826021 ERS1474295 ERP020578 PRJEB18632 RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf E-MTAB-5323 Transcriptome Analysis The aim of this analysis is to uncover novel molecules synthesized and secreted from cardiomyocytes. ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323   Protocols: To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs. Sample1 SAMEA27135418 Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27135418|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample1|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:Nls mCherryncv11Tg|sample name:E MTAB 5323:Sample1                 Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf E MTAB 5323:Sample1 s Sample1 s RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture’s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs. Experimental Factor: Tgmyl7:Nls mCherryncv11Tg:genotype RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiSeq   ERP020578 Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16 mochizukis_lab_myl7_NLSmCHerry_72h_02.fastq.gz fastq 766251339.0 10284347.0 E MTAB 5323:Sample1 1 0:0 1:74.51 A:214234414;C:174215653;G:180382062;T:197361982;N:57228 0 74     214234414 174215653 180382062 197361982 57228 ERX1826021 ERS1474295 ERA776061 Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive 1 0.87766   0.21561   0.77477   0.53919   73   B   usable mapping rate illumina miseq full_length poly_a nebnext bulk unknown unknown   Japan 2016-12-15 Larval Larval 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
10056 10056 ERR4691987 ERX4613068 ERS5216074 ERP124560 PRJEB40865 RNA seq of zebrafish adult MCU mutant hearts ena-STUDY-UCLA-16-10-2020-22:30:44:295-390 Other We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart. ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16     zebrafish adult heart RNA SAMEA7457891 UCLA ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457891|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:mcu mutant 2|common name:zebrafish|dev stage:adult|sample name:mcu mutant 2|scientific name:Danio rerio|tissue type:heart                 Illumina HiSeq 3000 sequencing ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 4 unspecified 1     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 3000   ERP124560 Illumina HiSeq 3000 sequencing ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21 MCU_2.fastq.gz fastq 1291626898.0 35072619.0 ena RUN UCLA 16 10 2020 22:30:43:819 4 0:36.83 1:0 A:364596432;C:305716590;G:295397140;T:324498501;N:1418235 36 0     364596432 305716590 295397140 324498501 1418235 ERX4613068 ERS5216074 ERA2987364 European Nucleotide Archive University of California, Los Angeles, USA 1 0.93311   0.08182   0.75852   0.54813   37   B   usable mapping rate illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2020-10-16 Adult Adult Heart Cardiovascular System
10057 10057 ERR4691986 ERX4613067 ERS5216073 ERP124560 PRJEB40865 RNA seq of zebrafish adult MCU mutant hearts ena-STUDY-UCLA-16-10-2020-22:30:44:295-390 Other We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart. ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16     zebrafish adult heart RNA SAMEA7457890 UCLA ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457890|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:mcu mutant 1|common name:zebrafish|dev stage:adult|sample name:mcu mutant 1|scientific name:Danio rerio|tissue type:heart                 Illumina HiSeq 3000 sequencing ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 3 unspecified 1     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 3000   ERP124560 Illumina HiSeq 3000 sequencing ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21 MCU_1.fastq.gz fastq 1236033124.0 33559740.0 ena RUN UCLA 16 10 2020 22:30:43:819 3 0:36.83 1:0 A:348518065;C:293502111;G:279181983;T:313506799;N:1324166 36 0     348518065 293502111 279181983 313506799 1324166 ERX4613067 ERS5216073 ERA2987364 European Nucleotide Archive University of California, Los Angeles, USA 1 0.92798   0.07907   0.7697   0.5488   37   B   usable mapping rate illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2020-10-16 Adult Adult Heart Cardiovascular System
10058 10058 ERR4691985 ERX4613066 ERS5216072 ERP124560 PRJEB40865 RNA seq of zebrafish adult MCU mutant hearts ena-STUDY-UCLA-16-10-2020-22:30:44:295-390 Other We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart. ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16     zebrafish adult heart RNA SAMEA7457889 UCLA ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457889|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:wildtype 2|common name:zebrafish|dev stage:adult|sample name:wildtype 2|scientific name:Danio rerio|tissue type:heart                 Illumina HiSeq 3000 sequencing ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 3000   ERP124560 Illumina HiSeq 3000 sequencing ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21 WT_2.fastq.gz fastq 1180831209.0 32069533.0 ena RUN UCLA 16 10 2020 22:30:43:819 2 0:36.82 1:0 A:328604642;C:281065336;G:278743466;T:291039015;N:1378750 36 0     328604642 281065336 278743466 291039015 1378750 ERX4613066 ERS5216072 ERA2987364 European Nucleotide Archive University of California, Los Angeles, USA 1 0.92319   0.08946   0.75706   0.49996   37   B   usable mapping rate illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2020-10-16 Adult Adult Heart Cardiovascular System
10059 10059 ERR4691984 ERX4613065 ERS5216071 ERP124560 PRJEB40865 RNA seq of zebrafish adult MCU mutant hearts ena-STUDY-UCLA-16-10-2020-22:30:44:295-390 Other We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart. ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16     zebrafish adult heart RNA SAMEA7457888 UCLA ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457888|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:wildtype 1|common name:zebrafish|dev stage:adult|sample name:wildtype 1|scientific name:Danio rerio|tissue type:heart                 Illumina HiSeq 3000 sequencing ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 3000   ERP124560 Illumina HiSeq 3000 sequencing ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21 WT_1.fastq.gz fastq 1428414407.0 38793098.0 ena RUN UCLA 16 10 2020 22:30:43:819 1 0:36.82 1:0 A:398925739;C:338731211;G:333527196;T:355553981;N:1676280 36 0     398925739 338731211 333527196 355553981 1676280 ERX4613065 ERS5216071 ERA2987364 European Nucleotide Archive University of California, Los Angeles, USA 1 0.92407   0.08758   0.75726   0.4969   37   B   usable mapping rate illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2020-10-16 Adult Adult Heart Cardiovascular System
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
25170 25170 SRR25661605 SRX21387413 SRS18627977 SRP455520 PRJNA1006302 The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes GSE241049 Transcriptome Analysis To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.   pubmed:39658721   hand2 FLD+/? 20 hpf CMs rep3 GSM7714404   source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing hand2 FLD+/? 20 hpf CMs rep3 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts embryonic heart   miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS GSM7714404 GSM7714404: hand2 FLD+/? 20 hpf CMs rep3; Danio rerio; RNA Seq GSM7714404 r1 GSM7714404 1 miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP455520   loader:fastq load.py E22_3458_Yanli_HT_Lib_WT_het_3_R1.fastq.gz fastq 2441736984.0 34141777.0 GSM7714404 r1 0:71.52 A:706186414;C:496261994;G:526176364;T:713112212;N:0 71       706186414 496261994 526176364 713112212 0 SRX21387413 SRS18627977 SRA1694205 MPI for heart and lung research MPI for heart and lung research 1 0.9026   0.15816   0.76278   0.44042   72   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Germany 2023-08-17 Segmentation Embryo Heart Cardiovascular System
25171 25171 SRR25661606 SRX21387412 SRS18627976 SRP455520 PRJNA1006302 The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes GSE241049 Transcriptome Analysis To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.   pubmed:39658721   hand2 FLD+/? 20 hpf CMs rep2 GSM7714403   source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing hand2 FLD+/? 20 hpf CMs rep2 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts embryonic heart   miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS GSM7714403 GSM7714403: hand2 FLD+/? 20 hpf CMs rep2; Danio rerio; RNA Seq GSM7714403 r1 GSM7714403 1 miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP455520   loader:fastq load.py E22_3458_Yanli_HT_Lib_WT_het_2_R1.fastq.gz fastq 2185611269.0 30558084.0 GSM7714403 r1 0:71.52 A:612617675;C:458632518;G:474458738;T:639902338;N:0 71       612617675 458632518 474458738 639902338 0 SRX21387412 SRS18627976 SRA1694205 MPI for heart and lung research MPI for heart and lung research 1 0.90042   0.14005   0.75424   0.44277   72   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Germany 2023-08-17 Segmentation Embryo Heart Cardiovascular System
25172 25172 SRR25661607 SRX21387411 SRS18627975 SRP455520 PRJNA1006302 The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes GSE241049 Transcriptome Analysis To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.   pubmed:39658721   hand2 FLD+/? 20 hpf CMs rep1 GSM7714402   source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing hand2 FLD+/? 20 hpf CMs rep1 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts embryonic heart   miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS GSM7714402 GSM7714402: hand2 FLD+/? 20 hpf CMs rep1; Danio rerio; RNA Seq GSM7714402 r1 GSM7714402 1 miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP455520   loader:fastq load.py E22_3458_Yanli_HT_Lib_WT_het_1_R1.fastq.gz fastq 2291884894.0 32043147.0 GSM7714402 r1 0:71.52 A:635094975;C:489594953;G:499909828;T:667285138;N:0 71       635094975 489594953 499909828 667285138 0 SRX21387411 SRS18627975 SRA1694205 MPI for heart and lung research MPI for heart and lung research 1 0.90883   0.14288   0.75331   0.44459   71   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Germany 2023-08-17 Segmentation Embryo Heart Cardiovascular System
25173 25173 SRR25661608 SRX21387410 SRS18627974 SRP455520 PRJNA1006302 The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes GSE241049 Transcriptome Analysis To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.   pubmed:39658721   WT 20 hpf CMs rep3 GSM7714401   source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing WT 20 hpf CMs rep3 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts embryonic heart   miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS GSM7714401 GSM7714401: WT 20 hpf CMs rep3; Danio rerio; RNA Seq GSM7714401 r1 GSM7714401 1 miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP455520   loader:fastq load.py E22_3458_Yanli_HT_Lib_WT_CMs_3_R1.fastq.gz fastq 2268251602.0 31717610.0 GSM7714401 r1 0:71.51 A:637196241;C:477782543;G:497683941;T:655588877;N:0 71       637196241 477782543 497683941 655588877 0 SRX21387410 SRS18627974 SRA1694205 MPI for heart and lung research MPI for heart and lung research 1 0.90026   0.13291   0.78707   0.40811   71   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Germany 2023-08-17 Segmentation Embryo Heart Cardiovascular System
25174 25174 SRR25661609 SRX21387409 SRS18627973 SRP455520 PRJNA1006302 The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes GSE241049 Transcriptome Analysis To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.   pubmed:39658721   WT 20 hpf CMs rep2 GSM7714400   source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing WT 20 hpf CMs rep2 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts embryonic heart   miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS GSM7714400 GSM7714400: WT 20 hpf CMs rep2; Danio rerio; RNA Seq GSM7714400 r1 GSM7714400 1 miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP455520   loader:fastq load.py E22_3458_Yanli_HT_Lib_WT_CMs_2_R1.fastq.gz fastq 2195524610.0 30700033.0 GSM7714400 r1 0:71.52 A:615401741;C:462686936;G:481135567;T:636300366;N:0 71       615401741 462686936 481135567 636300366 0 SRX21387409 SRS18627973 SRA1694205 MPI for heart and lung research MPI for heart and lung research 1 0.90323   0.1476   0.78744   0.41728   72   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Germany 2023-08-17 Segmentation Embryo Heart Cardiovascular System
25175 25175 SRR25661610 SRX21387408 SRS18627972 SRP455520 PRJNA1006302 The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes GSE241049 Transcriptome Analysis To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.   pubmed:39658721   WT 20 hpf CMs rep1 GSM7714399   source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing WT 20 hpf CMs rep1 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts embryonic heart   miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS GSM7714399 GSM7714399: WT 20 hpf CMs rep1; Danio rerio; RNA Seq GSM7714399 r1 GSM7714399 1 miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP455520   loader:fastq load.py E22_3458_Yanli_HT_Lib_WT_CMs_1_R1.fastq.gz fastq 2258160684.0 31576661.0 GSM7714399 r1 0:71.51 A:641254288;C:471580136;G:491501482;T:653824778;N:0 71       641254288 471580136 491501482 653824778 0 SRX21387408 SRS18627972 SRA1694205 MPI for heart and lung research MPI for heart and lung research 1 0.9   0.13993   0.78445   0.40575   72   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Germany 2023-08-17 Segmentation Embryo Heart Cardiovascular System
25176 25176 SRR25661611 SRX21387407 SRS18627971 SRP455520 PRJNA1006302 The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes GSE241049 Transcriptome Analysis To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.   pubmed:39658721   hand2 OE 20 hpf CMs rep3 GSM7714398   source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing hand2 OE 20 hpf CMs rep3 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts embryonic heart   miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS GSM7714398 GSM7714398: hand2 OE 20 hpf CMs rep3; Danio rerio; RNA Seq GSM7714398 r1 GSM7714398 1 miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP455520   loader:fastq load.py E22_3458_Yanli_HT_Lib_OE_CMs_3_R1.fastq.gz fastq 1886569909.0 26380170.0 GSM7714398 r1 0:71.51 A:534874421;C:392168718;G:411533838;T:547992932;N:0 71       534874421 392168718 411533838 547992932 0 SRX21387407 SRS18627971 SRA1694205 MPI for heart and lung research MPI for heart and lung research 1 0.89968   0.14763   0.77881   0.42601   72   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Germany 2023-08-17 Segmentation Embryo Heart Cardiovascular System
25177 25177 SRR25661612 SRX21387406 SRS18627970 SRP455520 PRJNA1006302 The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes GSE241049 Transcriptome Analysis To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.   pubmed:39658721   hand2 OE 20 hpf CMs rep2 GSM7714397   source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing hand2 OE 20 hpf CMs rep2 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts embryonic heart   miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS GSM7714397 GSM7714397: hand2 OE 20 hpf CMs rep2; Danio rerio; RNA Seq GSM7714397 r1 GSM7714397 1 miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP455520   loader:fastq load.py E22_3458_Yanli_HT_Lib_OE_CMs_2_R1.fastq.gz fastq 2197151812.0 30722639.0 GSM7714397 r1 0:71.52 A:617116635;C:461951919;G:481371246;T:636712012;N:0 71       617116635 461951919 481371246 636712012 0 SRX21387406 SRS18627970 SRA1694205 MPI for heart and lung research MPI for heart and lung research 1 0.90877   0.14744   0.77191   0.42845   72   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Germany 2023-08-17 Segmentation Embryo Heart Cardiovascular System
25178 25178 SRR25661613 SRX21387405 SRS18627969 SRP455520 PRJNA1006302 The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes GSE241049 Transcriptome Analysis To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.   pubmed:39658721   hand2 OE 20 hpf CMs rep1 GSM7714396   source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing hand2 OE 20 hpf CMs rep1 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts embryonic heart   miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS GSM7714396 GSM7714396: hand2 OE 20 hpf CMs rep1; Danio rerio; RNA Seq GSM7714396 r1 GSM7714396 1 miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP455520   loader:fastq load.py E22_3458_Yanli_HT_Lib_OE_CMs_1_R1.fastq.gz fastq 1773398936.0 24797998.0 GSM7714396 r1 0:71.51 A:495618212;C:375438077;G:390377060;T:511965587;N:0 71       495618212 375438077 390377060 511965587 0 SRX21387405 SRS18627969 SRA1694205 MPI for heart and lung research MPI for heart and lung research 1 0.90769   0.1387   0.7768   0.42096   72   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Germany 2023-08-17 Segmentation Embryo Heart Cardiovascular System
25179 25179 SRR25661614 SRX21387404 SRS18627968 SRP455520 PRJNA1006302 The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes GSE241049 Transcriptome Analysis To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.   pubmed:39658721   hand2 FLD / 20 hpf CMs rep3 GSM7714395   source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing hand2 FLD / 20 hpf CMs rep3 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts embryonic heart   miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS GSM7714395 GSM7714395: hand2 FLD / 20 hpf CMs rep3; Danio rerio; RNA Seq GSM7714395 r1 GSM7714395 1 miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP455520   loader:fastq load.py E22_3458_Yanli_HT_Lib_Mut_3_R1.fastq.gz fastq 2179400259.0 30471965.0 GSM7714395 r1 0:71.52 A:600555691;C:468535203;G:483122661;T:627186704;N:0 71       600555691 468535203 483122661 627186704 0 SRX21387404 SRS18627968 SRA1694205 MPI for heart and lung research MPI for heart and lung research 1 0.91581   0.12256   0.75209   0.43413   71   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Germany 2023-08-17 Segmentation Embryo Heart Cardiovascular System
25180 25180 SRR25661615 SRX21387403 SRS18627967 SRP455520 PRJNA1006302 The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes GSE241049 Transcriptome Analysis To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.   pubmed:39658721   hand2 FLD / 20 hpf CMs rep2 GSM7714394   source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing hand2 FLD / 20 hpf CMs rep2 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts embryonic heart   miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS GSM7714394 GSM7714394: hand2 FLD / 20 hpf CMs rep2; Danio rerio; RNA Seq GSM7714394 r1 GSM7714394 1 miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP455520   loader:fastq load.py E22_3458_Yanli_HT_Lib_Mut_2_R1.fastq.gz fastq 2340991168.0 32733068.0 GSM7714394 r1 0:71.52 A:647423337;C:500120073;G:514803152;T:678644606;N:0 71       647423337 500120073 514803152 678644606 0 SRX21387403 SRS18627967 SRA1694205 MPI for heart and lung research MPI for heart and lung research 1 0.91231   0.12561   0.75118   0.44445   71   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Germany 2023-08-17 Segmentation Embryo Heart Cardiovascular System
25181 25181 SRR25661616 SRX21387402 SRS18627966 SRP455520 PRJNA1006302 The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes GSE241049 Transcriptome Analysis To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.   pubmed:39658721   hand2 FLD / 20 hpf CMs rep1 GSM7714393   source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing hand2 FLD / 20 hpf CMs rep1 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts embryonic heart   miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS GSM7714393 GSM7714393: hand2 FLD / 20 hpf CMs rep1; Danio rerio; RNA Seq GSM7714393 r1 GSM7714393 1 miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP455520   loader:fastq load.py E22_3458_Yanli_HT_Lib_Mut_1_R1.fastq.gz fastq 2727863036.0 38140997.0 GSM7714393 r1 0:71.52 A:760867462;C:577539041;G:596986102;T:792470431;N:0 71       760867462 577539041 596986102 792470431 0 SRX21387402 SRS18627966 SRA1694205 MPI for heart and lung research MPI for heart and lung research 1 0.91175   0.1342   0.75282   0.44063   72   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Germany 2023-08-17 Segmentation Embryo Heart Cardiovascular System
29086 29086 SRR27015250 SRX22707800 SRS19700101 SRP475323 PRJNA1047551 Identification of genes important during atrial myocardial morphogenesis GSE249149 Transcriptome Analysis Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures. We aimed to identify the genes involved during this process and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.   pubmed:39289341   Wild type zebrafish atrial cardiomyocytes 72 hpf rep 3 GSM7927521   source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf loc name:missing|collection date:missing Wild type zebrafish atrial cardiomyocytes 72 hpf rep 3 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix embryonic heart   miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf GSM7927521 GSM7927521: Wild type zebrafish atrial cardiomyocytes 72 hpf rep 3; Danio rerio; RNA Seq GSM7927521 r1 GSM7927521 1 miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP475323   loader:fastq load.py dst226_zbrf_clt___ACrdmct-age___72h_b03_t01_m01_R1.fastq.gz fastq 1709509823.0 28403358.0 GSM7927521 r1 0:60.19 A:400293032;C:330429588;G:326652799;T:383291002;N:268843402 60       400293032 330429588 326652799 383291002 268843402 SRX22707800 SRS19700101 SRA1761360 MPI for heart and lung research MPI for heart and lung research 1 0.90079   0.0827   0.81406   0.64557   35   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Germany 2023-12-01 Larval Larval Heart Cardiovascular System
29087 29087 SRR27015251 SRX22707799 SRS19700100 SRP475323 PRJNA1047551 Identification of genes important during atrial myocardial morphogenesis GSE249149 Transcriptome Analysis Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures. We aimed to identify the genes involved during this process and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.   pubmed:39289341   Wild type zebrafish atrial cardiomyocytes 72 hpf rep 2 GSM7927520   source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf loc name:missing|collection date:missing Wild type zebrafish atrial cardiomyocytes 72 hpf rep 2 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix embryonic heart   miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf GSM7927520 GSM7927520: Wild type zebrafish atrial cardiomyocytes 72 hpf rep 2; Danio rerio; RNA Seq GSM7927520 r1 GSM7927520 1 miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP475323   loader:fastq load.py dst226_zbrf_clt___ACrdmct-age___72h_b02_t01_m01_R1.fastq.gz fastq 1740891025.0 28211981.0 GSM7927520 r1 0:61.71 A:419094150;C:347792831;G:345450108;T:407537501;N:221016435 61       419094150 347792831 345450108 407537501 221016435 SRX22707799 SRS19700100 SRA1761360 MPI for heart and lung research MPI for heart and lung research 1 0.90091   0.13293   0.78464   0.54281   69   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Germany 2023-12-01 Larval Larval Heart Cardiovascular System
29088 29088 SRR27015252 SRX22707798 SRS19700099 SRP475323 PRJNA1047551 Identification of genes important during atrial myocardial morphogenesis GSE249149 Transcriptome Analysis Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures. We aimed to identify the genes involved during this process and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.   pubmed:39289341   Wild type zebrafish atrial cardiomyocytes 72 hpf rep 1 GSM7927519   source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf loc name:missing|collection date:missing Wild type zebrafish atrial cardiomyocytes 72 hpf rep 1 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix embryonic heart   miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf GSM7927519 GSM7927519: Wild type zebrafish atrial cardiomyocytes 72 hpf rep 1; Danio rerio; RNA Seq GSM7927519 r1 GSM7927519 1 miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP475323   loader:fastq load.py dst226_zbrf_clt___ACrdmct-age___72h_b01_t01_m01_R1.fastq.gz fastq 1930552948.0 30996774.0 GSM7927519 r1 0:62.28 A:468769814;C:389869994;G:387622687;T:454801262;N:229489191 62       468769814 389869994 387622687 454801262 229489191 SRX22707798 SRS19700099 SRA1761360 MPI for heart and lung research MPI for heart and lung research 1 0.90465   0.10656   0.79586   0.55674   72   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Germany 2023-12-01 Larval Larval Heart Cardiovascular System
29089 29089 SRR27015253 SRX22707797 SRS19700098 SRP475323 PRJNA1047551 Identification of genes important during atrial myocardial morphogenesis GSE249149 Transcriptome Analysis Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures. We aimed to identify the genes involved during this process and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.   pubmed:39289341   Wild type zebrafish atrial cardiomyocytes 48 hpf rep 3 GSM7927518   source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf loc name:missing|collection date:missing Wild type zebrafish atrial cardiomyocytes 48 hpf rep 3 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix embryonic heart   miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf GSM7927518 GSM7927518: Wild type zebrafish atrial cardiomyocytes 48 hpf rep 3; Danio rerio; RNA Seq GSM7927518 r1 GSM7927518 1 miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP475323   loader:fastq load.py dst226_zbrf_clt___ACrdmct-age___48h_b03_t01_m01_R1.fastq.gz fastq 2161847345.0 35921817.0 GSM7927518 r1 0:60.18 A:505467877;C:418329045;G:416403136;T:483063599;N:338583688 60       505467877 418329045 416403136 483063599 338583688 SRX22707797 SRS19700098 SRA1761360 MPI for heart and lung research MPI for heart and lung research 1 0.89532   0.08355   0.82012   0.68413   35   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Germany 2023-12-01 Hatching Embryo Heart Cardiovascular System
29090 29090 SRR27015254 SRX22707796 SRS19700097 SRP475323 PRJNA1047551 Identification of genes important during atrial myocardial morphogenesis GSE249149 Transcriptome Analysis Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures. We aimed to identify the genes involved during this process and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.   pubmed:39289341   Wild type zebrafish atrial cardiomyocytes 48 hpf rep 2 GSM7927517   source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf loc name:missing|collection date:missing Wild type zebrafish atrial cardiomyocytes 48 hpf rep 2 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix embryonic heart   miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf GSM7927517 GSM7927517: Wild type zebrafish atrial cardiomyocytes 48 hpf rep 2; Danio rerio; RNA Seq GSM7927517 r1 GSM7927517 1 miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP475323   loader:fastq load.py dst226_zbrf_clt___ACrdmct-age___48h_b02_t01_m01_R1.fastq.gz fastq 2065547064.0 31863833.0 GSM7927517 r1 0:64.82 A:530497695;C:434164388;G:434118538;T:518043928;N:148722515 64       530497695 434164388 434118538 518043928 148722515 SRX22707796 SRS19700097 SRA1761360 MPI for heart and lung research MPI for heart and lung research 1 0.91772   0.17863   0.76828   0.49567   72   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Germany 2023-12-01 Hatching Embryo Heart Cardiovascular System
29091 29091 SRR27015255 SRX22707795 SRS19700096 SRP475323 PRJNA1047551 Identification of genes important during atrial myocardial morphogenesis GSE249149 Transcriptome Analysis Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures. We aimed to identify the genes involved during this process and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.   pubmed:39289341   Wild type zebrafish atrial cardiomyocytes 48 hpf rep 1 GSM7927516   source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf loc name:missing|collection date:missing Wild type zebrafish atrial cardiomyocytes 48 hpf rep 1 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix embryonic heart   miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf GSM7927516 GSM7927516: Wild type zebrafish atrial cardiomyocytes 48 hpf rep 1; Danio rerio; RNA Seq GSM7927516 r1 GSM7927516 1 miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP475323   loader:fastq load.py dst226_zbrf_clt___ACrdmct-age___48h_b01_t01_m01_R1.fastq.gz fastq 1619268089.0 24941754.0 GSM7927516 r1 0:64.92 A:410578311;C:344485123;G:343852178;T:401558739;N:118793738 64       410578311 344485123 343852178 401558739 118793738 SRX22707795 SRS19700096 SRA1761360 MPI for heart and lung research MPI for heart and lung research 1 0.91693   0.13175   0.77082   0.47511   72   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Germany 2023-12-01 Hatching Embryo Heart Cardiovascular System
29569 29569 SRR27368685 SRX23045203 SRS20006222 SRP480346 PRJNA1057908 An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq] GSE252151 Transcriptome Analysis cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types predominantly cardiomyocytes. Therefore cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development as they share a number of physiological features with the human heart during development. Therefore we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes validating these genomic regions as cardiac regulatory elements. We share this comprehensive reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells n=3 biological replicates and GFP negative cells 500 000 cells n=3 biological replicates were collected and RNA sequencing was performed on these samples. parent bioproject:PRJNA1057890     500kGFPneg6 Non cardiomyocytes GSM7995233   source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control|geo loc name:missing|collection date:missing 500kGFPneg6 Non cardiomyocytes FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin 2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al 2018 using default parameters. There were two sets of counts obtained the first were the reads mapped to genome Zv9 and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9 Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample Heart   RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control GSM7995233 GSM7995233: 500kGFPneg6 Non cardiomyocytes; Danio rerio; RNA Seq GSM7995233 r1 GSM7995233 1 RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP480346     500kGFPneg6_S42_L008_R1_001.fastq.gz fastq 527477356.0 10449387.0 GSM7995233 r1 0:50.48 A:141759410;C:113279303;G:116384028;T:155860577;N:194038 50       141759410 113279303 116384028 155860577 194038 SRX23045203 SRS20006222 SRA1776396 Australian Regenerative Medicine Institute, Monash University Australian Regenerative Medicine Institute, Monash University 1 0.79175   0.2711   0.7587   0.61924   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-12-27 Undetermined Larval Heart Cardiovascular System
29570 29570 SRR27368686 SRX23045202 SRS20006221 SRP480346 PRJNA1057908 An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq] GSE252151 Transcriptome Analysis cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types predominantly cardiomyocytes. Therefore cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development as they share a number of physiological features with the human heart during development. Therefore we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes validating these genomic regions as cardiac regulatory elements. We share this comprehensive reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells n=3 biological replicates and GFP negative cells 500 000 cells n=3 biological replicates were collected and RNA sequencing was performed on these samples. parent bioproject:PRJNA1057890     500kGFPneg5 Non cardiomyocytes GSM7995232   source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control|geo loc name:missing|collection date:missing 500kGFPneg5 Non cardiomyocytes FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin 2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al 2018 using default parameters. There were two sets of counts obtained the first were the reads mapped to genome Zv9 and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9 Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample Heart   RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control GSM7995232 GSM7995232: 500kGFPneg5 Non cardiomyocytes; Danio rerio; RNA Seq GSM7995232 r1 GSM7995232 1 RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP480346     500kGFPneg5_S41_L008_R1_001.fastq.gz fastq 3356204764.0 66511806.0 GSM7995232 r1 0:50.46 A:860342578;C:766593257;G:774473426;T:953992775;N:802728 50       860342578 766593257 774473426 953992775 802728 SRX23045202 SRS20006221 SRA1776396 Australian Regenerative Medicine Institute, Monash University Australian Regenerative Medicine Institute, Monash University 1 0.70469   0.23332   0.76992   0.62712   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-12-27 Undetermined Larval Heart Cardiovascular System
29571 29571 SRR27368687 SRX23045201 SRS20006220 SRP480346 PRJNA1057908 An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq] GSE252151 Transcriptome Analysis cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types predominantly cardiomyocytes. Therefore cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development as they share a number of physiological features with the human heart during development. Therefore we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes validating these genomic regions as cardiac regulatory elements. We share this comprehensive reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells n=3 biological replicates and GFP negative cells 500 000 cells n=3 biological replicates were collected and RNA sequencing was performed on these samples. parent bioproject:PRJNA1057890     500kGFPneg4 Non cardiomyocytes GSM7995231   source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control|geo loc name:missing|collection date:missing 500kGFPneg4 Non cardiomyocytes FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin 2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al 2018 using default parameters. There were two sets of counts obtained the first were the reads mapped to genome Zv9 and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9 Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample Heart   RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control GSM7995231 GSM7995231: 500kGFPneg4 Non cardiomyocytes; Danio rerio; RNA Seq GSM7995231 r1 GSM7995231 1 RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP480346     500kGFPneg4_S40_L008_R1_001.fastq.gz fastq 3075367681.0 60986692.0 GSM7995231 r1 0:50.43 A:807059039;C:682279458;G:696326840;T:888937765;N:764579 50       807059039 682279458 696326840 888937765 764579 SRX23045201 SRS20006220 SRA1776396 Australian Regenerative Medicine Institute, Monash University Australian Regenerative Medicine Institute, Monash University 1 0.74255   0.26699   0.76786   0.63053   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-12-27 Undetermined Larval Heart Cardiovascular System
29572 29572 SRR27368688 SRX23045200 SRS20006219 SRP480346 PRJNA1057908 An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq] GSE252151 Transcriptome Analysis cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types predominantly cardiomyocytes. Therefore cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development as they share a number of physiological features with the human heart during development. Therefore we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes validating these genomic regions as cardiac regulatory elements. We share this comprehensive reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells n=3 biological replicates and GFP negative cells 500 000 cells n=3 biological replicates were collected and RNA sequencing was performed on these samples. parent bioproject:PRJNA1057890     30kGFPpos3 Cardiomyocytes GSM7995230   source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control|geo loc name:missing|collection date:missing 30kGFPpos3 Cardiomyocytes FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin 2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al 2018 using default parameters. There were two sets of counts obtained the first were the reads mapped to genome Zv9 and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9 Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample Heart   RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control GSM7995230 GSM7995230: 30kGFPpos3 Cardiomyocytes; Danio rerio; RNA Seq GSM7995230 r1 GSM7995230 1 RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP480346     30kGFPpos3_S39_L008_R1_001.fastq.gz fastq 2938808771.0 58361915.0 GSM7995230 r1 0:50.35 A:533261626;C:883704329;G:825929620;T:694986734;N:926462 50       533261626 883704329 825929620 694986734 926462 SRX23045200 SRS20006219 SRA1776396 Australian Regenerative Medicine Institute, Monash University Australian Regenerative Medicine Institute, Monash University 1 0.12924   0.05415   0.92034   0.70896   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-12-27 Undetermined Larval Heart Cardiovascular System
29573 29573 SRR27368689 SRX23045199 SRS20006218 SRP480346 PRJNA1057908 An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq] GSE252151 Transcriptome Analysis cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types predominantly cardiomyocytes. Therefore cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development as they share a number of physiological features with the human heart during development. Therefore we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes validating these genomic regions as cardiac regulatory elements. We share this comprehensive reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells n=3 biological replicates and GFP negative cells 500 000 cells n=3 biological replicates were collected and RNA sequencing was performed on these samples. parent bioproject:PRJNA1057890     30kGFPpos2 Cardiomyocytes GSM7995229   source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control|geo loc name:missing|collection date:missing 30kGFPpos2 Cardiomyocytes FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin 2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al 2018 using default parameters. There were two sets of counts obtained the first were the reads mapped to genome Zv9 and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9 Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample Heart   RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control GSM7995229 GSM7995229: 30kGFPpos2 Cardiomyocytes; Danio rerio; RNA Seq GSM7995229 r1 GSM7995229 1 RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP480346     30kGFPpos2_S38_L008_R1_001.fastq.gz fastq 3006409096.0 59645543.0 GSM7995229 r1 0:50.40 A:560839480;C:885691877;G:830121593;T:728932219;N:823927 50       560839480 885691877 830121593 728932219 823927 SRX23045199 SRS20006218 SRA1776396 Australian Regenerative Medicine Institute, Monash University Australian Regenerative Medicine Institute, Monash University 1 0.17805   0.06115   0.89769   0.68731   49   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-12-27 Undetermined Larval Heart Cardiovascular System
29574 29574 SRR27368690 SRX23045198 SRS20006217 SRP480346 PRJNA1057908 An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq] GSE252151 Transcriptome Analysis cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types predominantly cardiomyocytes. Therefore cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development as they share a number of physiological features with the human heart during development. Therefore we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes validating these genomic regions as cardiac regulatory elements. We share this comprehensive reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells n=3 biological replicates and GFP negative cells 500 000 cells n=3 biological replicates were collected and RNA sequencing was performed on these samples. parent bioproject:PRJNA1057890     30kGFPpos1 Cardiomyocytes GSM7995228   source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control|geo loc name:missing|collection date:missing 30kGFPpos1 Cardiomyocytes FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin 2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al 2018 using default parameters. There were two sets of counts obtained the first were the reads mapped to genome Zv9 and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9 Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample Heart   RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control GSM7995228 GSM7995228: 30kGFPpos1 Cardiomyocytes; Danio rerio; RNA Seq GSM7995228 r1 GSM7995228 1 RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP480346     30kGFPpos1_S37_L008_R1_001.fastq.gz fastq 3254639839.0 64665631.0 GSM7995228 r1 0:50.33 A:545193535;C:1023804678;G:938318027;T:746302007;N:1021592 50       545193535 1023804678 938318027 746302007 1021592 SRX23045198 SRS20006217 SRA1776396 Australian Regenerative Medicine Institute, Monash University Australian Regenerative Medicine Institute, Monash University 1 0.05453   0.01921   0.9643   0.78064   49   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-12-27 Undetermined Larval Heart Cardiovascular System
30006 30006 SRR27663958 SRX23331822 SRS20194274 SRP484810 PRJNA1066877 p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation GSE253758 Transcriptome Analysis While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.   pubmed:39242546   NFKB biol rep 3 GSM8027552   tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB sorted|geo loc name:missing|collection date:missing NFKB biol rep 3 Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene endothelial cells 22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer. RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440. Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle. cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB sorted GSM8027552 GSM8027552: NFKB biol rep 3; Danio rerio; RNA Seq GSM8027552 r1 GSM8027552 1 RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484810   loader:fastq load.py 6-RNA-1001_S6_L001_R1_001.fastq.gz fastq 7566894200.0 75668942.0 GSM8027552 r1 0:100 A:2055514007;C:1776454819;G:1779667416;T:1955100553;N:157405 100       2055514007 1776454819 1779667416 1955100553 157405 SRX23331822 SRS20194274 SRA1788753 Iowa State University Iowa State University                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2024-01-19 Multi-stage Multi-stage Endothelium Cardiovascular System
30007 30007 SRR27663959 SRX23331821 SRS20194275 SRP484810 PRJNA1066877 p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation GSE253758 Transcriptome Analysis While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.   pubmed:39242546   NFKB biol rep 2 GSM8027551   tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB sorted|geo loc name:missing|collection date:missing NFKB biol rep 2 Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene endothelial cells 22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer. RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440. Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle. cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB sorted GSM8027551 GSM8027551: NFKB biol rep 2; Danio rerio; RNA Seq GSM8027551 r1 GSM8027551 1 RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484810   loader:fastq load.py 5-RNA-0901_S5_L001_R1_001.fastq.gz fastq 8077393600.0 80773936.0 GSM8027551 r1 0:100 A:2195547260;C:1863472493;G:1887149224;T:2131055526;N:169097 100       2195547260 1863472493 1887149224 2131055526 169097 SRX23331821 SRS20194275 SRA1788753 Iowa State University Iowa State University                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2024-01-19 Multi-stage Multi-stage Endothelium Cardiovascular System
30008 30008 SRR27663960 SRX23331820 SRS20194273 SRP484810 PRJNA1066877 p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation GSE253758 Transcriptome Analysis While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.   pubmed:39242546   NFKB biol rep 1 GSM8027550   tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB sorted|geo loc name:missing|collection date:missing NFKB biol rep 1 Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene endothelial cells 22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer. RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440. Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle. cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB sorted GSM8027550 GSM8027550: NFKB biol rep 1; Danio rerio; RNA Seq GSM8027550 r1 GSM8027550 1 RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484810   loader:fastq load.py 4-RNA-1001_S4_L001_R1_001.fastq.gz fastq 6536957300.0 65369573.0 GSM8027550 r1 0:100 A:1764502914;C:1531091007;G:1533764634;T:1707464708;N:134037 100       1764502914 1531091007 1533764634 1707464708 134037 SRX23331820 SRS20194273 SRA1788753 Iowa State University Iowa State University                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2024-01-19 Multi-stage Multi-stage Endothelium Cardiovascular System
30009 30009 SRR27663961 SRX23331819 SRS20194272 SRP484810 PRJNA1066877 p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation GSE253758 Transcriptome Analysis While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.   pubmed:39242546   NFKB+ biol rep 3 GSM8027549   tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted|geo loc name:missing|collection date:missing NFKB+ biol rep 3 Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene endothelial cells 22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer. RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440. Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle. cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted GSM8027549 GSM8027549: NFKB+ biol rep 3; Danio rerio; RNA Seq GSM8027549 r1 GSM8027549 1 RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484810   loader:fastq load.py 3-RNA-1001_S3_L001_R1_001.fastq.gz fastq 10375249700.0 103752497.0 GSM8027549 r1 0:100 A:2873369145;C:2335823279;G:2356855554;T:2808985435;N:216287 100       2873369145 2335823279 2356855554 2808985435 216287 SRX23331819 SRS20194272 SRA1788753 Iowa State University Iowa State University                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2024-01-19 Multi-stage Multi-stage Endothelium Cardiovascular System
30010 30010 SRR27663962 SRX23331818 SRS20194271 SRP484810 PRJNA1066877 p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation GSE253758 Transcriptome Analysis While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.   pubmed:39242546   NFKB+ biol rep 2 GSM8027548   tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted|geo loc name:missing|collection date:missing NFKB+ biol rep 2 Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene endothelial cells 22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer. RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440. Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle. cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted GSM8027548 GSM8027548: NFKB+ biol rep 2; Danio rerio; RNA Seq GSM8027548 r1 GSM8027548 1 RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484810   loader:fastq load.py 2-RNA-1001_S2_L001_R1_001.fastq.gz fastq 5743794100.0 57437941.0 GSM8027548 r1 0:100 A:1588561398;C:1297479370;G:1310669617;T:1546965673;N:118042 100       1588561398 1297479370 1310669617 1546965673 118042 SRX23331818 SRS20194271 SRA1788753 Iowa State University Iowa State University                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2024-01-19 Multi-stage Multi-stage Endothelium Cardiovascular System
30011 30011 SRR27663963 SRX23331817 SRS20194270 SRP484810 PRJNA1066877 p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation GSE253758 Transcriptome Analysis While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.   pubmed:39242546   NFKB+ biol rep 1 GSM8027547   tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted|geo loc name:missing|collection date:missing NFKB+ biol rep 1 Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene endothelial cells 22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer. RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440. Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle. cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted GSM8027547 GSM8027547: NFKB+ biol rep 1; Danio rerio; RNA Seq GSM8027547 r1 GSM8027547 1 RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484810   loader:fastq load.py 1-RNA-0917_S1_L001_R1_001.fastq.gz fastq 6201542500.0 62015425.0 GSM8027547 r1 0:100 A:1696049302;C:1431941155;G:1441395671;T:1632027072;N:129300 100       1696049302 1431941155 1441395671 1632027072 129300 SRX23331817 SRS20194270 SRA1788753 Iowa State University Iowa State University                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2024-01-19 Multi-stage Multi-stage Endothelium Cardiovascular System
30512 30512 SRR27764782 SRX23429747 SRS20284188 SRP486526 PRJNA1070616 Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response GSE254466 Transcriptome Analysis The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l also known as Scaf1 promotes CIII CIV super assembly and energetic efficiency in zebrafish mice and humans. Here we studied the role of a second member of the Cox7a family Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism. Already in homeostatic conditions cox7a1 / hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical revealing that there is a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 / mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq. 4 pools each comprising 5 ventricles were sequenced per condition.   pubmed:38701784   Cardiac ventricle cox7a1 / replicate 4 GSM8042779   source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing Cardiac ventricle cox7a1 / replicate 4 Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts tab seprated values Cardiac Ventricle   4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol   tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury GSM8042779 GSM8042779: Cardiac ventricle cox7a1 / replicate 4; Danio rerio; RNA Seq GSM8042779 r1 GSM8042779 1 4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP486526     KO_10_Directional_S8_R1_001.fastq.gz fastq 8619450300.0 86194503.0 GSM8042779 r1 0:100 A:2183264320;C:2042597849;G:2002385828;T:2389908983;N:1293320 100       2183264320 2042597849 2002385828 2389908983 1293320 SRX23429747 SRS20284188 SRA1793874 University of Bern University of Bern                       B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified nebnext bulk unknown unknown   Switzerland 2024-01-29 Undetermined Adult Heart Cardiovascular System
30513 30513 SRR27764783 SRX23429746 SRS20284187 SRP486526 PRJNA1070616 Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response GSE254466 Transcriptome Analysis The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l also known as Scaf1 promotes CIII CIV super assembly and energetic efficiency in zebrafish mice and humans. Here we studied the role of a second member of the Cox7a family Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism. Already in homeostatic conditions cox7a1 / hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical revealing that there is a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 / mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq. 4 pools each comprising 5 ventricles were sequenced per condition.   pubmed:38701784   Cardiac ventricle cox7a1 / replicate 3 GSM8042778   source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing Cardiac ventricle cox7a1 / replicate 3 Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts tab seprated values Cardiac Ventricle   4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol   tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury GSM8042778 GSM8042778: Cardiac ventricle cox7a1 / replicate 3; Danio rerio; RNA Seq GSM8042778 r1 GSM8042778 1 4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP486526     KO_9_Directional_S7_R1_001.fastq.gz fastq 6466746100.0 64667461.0 GSM8042778 r1 0:100 A:1708351950;C:1464168743;G:1452219209;T:1841033764;N:972434 100       1708351950 1464168743 1452219209 1841033764 972434 SRX23429746 SRS20284187 SRA1793874 University of Bern University of Bern                       B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified nebnext bulk unknown unknown   Switzerland 2024-01-29 Undetermined Adult Heart Cardiovascular System
30514 30514 SRR27764784 SRX23429745 SRS20284186 SRP486526 PRJNA1070616 Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response GSE254466 Transcriptome Analysis The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l also known as Scaf1 promotes CIII CIV super assembly and energetic efficiency in zebrafish mice and humans. Here we studied the role of a second member of the Cox7a family Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism. Already in homeostatic conditions cox7a1 / hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical revealing that there is a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 / mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq. 4 pools each comprising 5 ventricles were sequenced per condition.   pubmed:38701784   Cardiac ventricle cox7a1 / replicate 2 GSM8042777   source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing Cardiac ventricle cox7a1 / replicate 2 Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts tab seprated values Cardiac Ventricle   4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol   tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury GSM8042777 GSM8042777: Cardiac ventricle cox7a1 / replicate 2; Danio rerio; RNA Seq GSM8042777 r1 GSM8042777 1 4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP486526     KO_8_Directional_S6_R1_001.fastq.gz fastq 6766795300.0 67667953.0 GSM8042777 r1 0:100 A:1803038642;C:1540664299;G:1518741633;T:1903355305;N:995421 100       1803038642 1540664299 1518741633 1903355305 995421 SRX23429745 SRS20284186 SRA1793874 University of Bern University of Bern                       B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified nebnext bulk unknown unknown   Switzerland 2024-01-29 Undetermined Adult Heart Cardiovascular System
30515 30515 SRR27764785 SRX23429744 SRS20284185 SRP486526 PRJNA1070616 Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response GSE254466 Transcriptome Analysis The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l also known as Scaf1 promotes CIII CIV super assembly and energetic efficiency in zebrafish mice and humans. Here we studied the role of a second member of the Cox7a family Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism. Already in homeostatic conditions cox7a1 / hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical revealing that there is a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 / mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq. 4 pools each comprising 5 ventricles were sequenced per condition.   pubmed:38701784   Cardiac ventricle cox7a1 / replicate 1 GSM8042776   source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing Cardiac ventricle cox7a1 / replicate 1 Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts tab seprated values Cardiac Ventricle   4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol   tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury GSM8042776 GSM8042776: Cardiac ventricle cox7a1 / replicate 1; Danio rerio; RNA Seq GSM8042776 r1 GSM8042776 1 4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP486526     KO_7_Directional_S5_R1_001.fastq.gz fastq 5583049300.0 55830493.0 GSM8042776 r1 0:100 A:1479820662;C:1265599242;G:1251078421;T:1585727832;N:823143 100       1479820662 1265599242 1251078421 1585727832 823143 SRX23429744 SRS20284185 SRA1793874 University of Bern University of Bern                       B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified nebnext bulk unknown unknown   Switzerland 2024-01-29 Undetermined Adult Heart Cardiovascular System
30516 30516 SRR27764786 SRX23429743 SRS20284184 SRP486526 PRJNA1070616 Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response GSE254466 Transcriptome Analysis The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l also known as Scaf1 promotes CIII CIV super assembly and energetic efficiency in zebrafish mice and humans. Here we studied the role of a second member of the Cox7a family Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism. Already in homeostatic conditions cox7a1 / hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical revealing that there is a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 / mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq. 4 pools each comprising 5 ventricles were sequenced per condition.   pubmed:38701784   Cardiac ventricle wt sibling replicate 4 GSM8042775   source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing Cardiac ventricle wt sibling replicate 4 Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts tab seprated values Cardiac Ventricle   4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol   tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury GSM8042775 GSM8042775: Cardiac ventricle wt sibling replicate 4; Danio rerio; RNA Seq GSM8042775 r1 GSM8042775 1 4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP486526     WT_5_Directional_S4_R1_001.fastq.gz fastq 6851217800.0 68512178.0 GSM8042775 r1 0:100 A:1837112549;C:1539284911;G:1515596368;T:1958221274;N:1002698 100       1837112549 1539284911 1515596368 1958221274 1002698 SRX23429743 SRS20284184 SRA1793874 University of Bern University of Bern                       B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified nebnext bulk unknown unknown   Switzerland 2024-01-29 Undetermined Adult Heart Cardiovascular System
30517 30517 SRR27764787 SRX23429742 SRS20284183 SRP486526 PRJNA1070616 Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response GSE254466 Transcriptome Analysis The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l also known as Scaf1 promotes CIII CIV super assembly and energetic efficiency in zebrafish mice and humans. Here we studied the role of a second member of the Cox7a family Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism. Already in homeostatic conditions cox7a1 / hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical revealing that there is a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 / mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq. 4 pools each comprising 5 ventricles were sequenced per condition.   pubmed:38701784   Cardiac ventricle wt sibling replicate 3 GSM8042774   source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing Cardiac ventricle wt sibling replicate 3 Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts tab seprated values Cardiac Ventricle   4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol   tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury GSM8042774 GSM8042774: Cardiac ventricle wt sibling replicate 3; Danio rerio; RNA Seq GSM8042774 r1 GSM8042774 1 4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP486526     WT_3_Directional_S3_R1_001.fastq.gz fastq 7036251700.0 70362517.0 GSM8042774 r1 0:100 A:1881612688;C:1574593657;G:1570342252;T:2008668471;N:1034632 100       1881612688 1574593657 1570342252 2008668471 1034632 SRX23429742 SRS20284183 SRA1793874 University of Bern University of Bern                       B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified nebnext bulk unknown unknown   Switzerland 2024-01-29 Undetermined Adult Heart Cardiovascular System
30518 30518 SRR27764788 SRX23429741 SRS20284182 SRP486526 PRJNA1070616 Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response GSE254466 Transcriptome Analysis The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l also known as Scaf1 promotes CIII CIV super assembly and energetic efficiency in zebrafish mice and humans. Here we studied the role of a second member of the Cox7a family Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism. Already in homeostatic conditions cox7a1 / hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical revealing that there is a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 / mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq. 4 pools each comprising 5 ventricles were sequenced per condition.   pubmed:38701784   Cardiac ventricle wt sibling replicate 2 GSM8042773   source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing Cardiac ventricle wt sibling replicate 2 Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts tab seprated values Cardiac Ventricle   4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol   tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury GSM8042773 GSM8042773: Cardiac ventricle wt sibling replicate 2; Danio rerio; RNA Seq GSM8042773 r1 GSM8042773 1 4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP486526     WT_2_Directional_S2_R1_001.fastq.gz fastq 6856428200.0 68564282.0 GSM8042773 r1 0:100 A:1790369167;C:1572129686;G:1566120109;T:1926782247;N:1026991 100       1790369167 1572129686 1566120109 1926782247 1026991 SRX23429741 SRS20284182 SRA1793874 University of Bern University of Bern                       B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified nebnext bulk unknown unknown   Switzerland 2024-01-29 Undetermined Adult Heart Cardiovascular System
30519 30519 SRR27764789 SRX23429740 SRS20284181 SRP486526 PRJNA1070616 Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response GSE254466 Transcriptome Analysis The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l also known as Scaf1 promotes CIII CIV super assembly and energetic efficiency in zebrafish mice and humans. Here we studied the role of a second member of the Cox7a family Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism. Already in homeostatic conditions cox7a1 / hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical revealing that there is a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 / mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq. 4 pools each comprising 5 ventricles were sequenced per condition.   pubmed:38701784   Cardiac ventricle wt sibling replicate 1 GSM8042772   source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing Cardiac ventricle wt sibling replicate 1 Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts tab seprated values Cardiac Ventricle   4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol   tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury GSM8042772 GSM8042772: Cardiac ventricle wt sibling replicate 1; Danio rerio; RNA Seq GSM8042772 r1 GSM8042772 1 4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP486526     WT_1_Directional_S1_R1_001.fastq.gz fastq 7089416800.0 70894168.0 GSM8042772 r1 0:100 A:1855346146;C:1626812736;G:1599932420;T:2006283874;N:1041624 100       1855346146 1626812736 1599932420 2006283874 1041624 SRX23429740 SRS20284181 SRA1793874 University of Bern University of Bern                       B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified nebnext bulk unknown unknown   Switzerland 2024-01-29 Undetermined 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

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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");;