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2,196 rows where experiment.library_layout = "PAIRED", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Heart"

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experiment.library_selection 10

technology 8

devstage_curation 8

devstage_curation_coarse 6

experiment.platform 3

tissue_curation_coarse 1

tissue_curation 1

  • Heart · 2,196 ✖

experiment.library_strategy 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 2,196 ✖

experiment.library_layout 1

  • PAIRED · 2,196 ✖
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
4359 4359 ERR1427424 ERX1497956 ERS1183258 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#91 SAMEA4012148 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012148|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#91|broker name:ArrayExpress|common name:zebrafish|fsc:25859|gfp:119|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#91|ssc:10090|tissue:Heart|well:C12                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#91 LCK 7#91 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 25859:fsc|Experimental Factor: 10090:ssc|Experimental Factor: 119:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_91_mod.bam LCK_7_91.cram bam cram     E MTAB 4617:LCK 7#91 0:125 1:125 A:115117295;C:110480558;G:102056870;T:121829131;N:52646 125 125     115117295 110480558 102056870 121829131 52646 ERX1497956   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.2053 0.20024 0.06111 0.05989 0.98019 0.98058 0.56103 0.56868 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4360 4360 ERR1427423 ERX1497955 ERS1183257 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#90 SAMEA4012147 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012147|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#90|broker name:ArrayExpress|common name:zebrafish|fsc:22987|gfp:178|individual:2|pi:6|plate:7|sample name:E MTAB 4617:LCK 7#90|ssc:6327|tissue:Heart|well:B12                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#90 LCK 7#90 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 22987:fsc|Experimental Factor: 6327:ssc|Experimental Factor: 178:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_90_mod.bam LCK_7_90.cram bam cram     E MTAB 4617:LCK 7#90 0:125 1:125 A:106342222;C:98049090;G:91971650;T:111243138;N:46400 125 125     106342222 98049090 91971650 111243138 46400 ERX1497955   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.2785 0.27322 0.08361 0.08291 0.97619 0.97703 0.60537 0.61379 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4361 4361 ERR1427422 ERX1497954 ERS1183256 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#9 SAMEA4012146 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012146|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#9|broker name:ArrayExpress|common name:zebrafish|fsc:24861|gfp:531|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#9|ssc:5852|tissue:Heart|well:A2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#9 LCK 7#9 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 24861:fsc|Experimental Factor: 5852:ssc|Experimental Factor: 531:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_9_mod.bam LCK_7_9.cram bam cram     E MTAB 4617:LCK 7#9 0:125 1:125 A:99732231;C:96455828;G:89233454;T:105851298;N:47439 125 125     99732231 96455828 89233454 105851298 47439 ERX1497954   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.21894 0.21406 0.0599 0.05904 0.97861 0.97877 0.57755 0.57546 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4362 4362 ERR1427421 ERX1497953 ERS1183255 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#89 SAMEA4012145 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012145|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#89|broker name:ArrayExpress|common name:zebrafish|fsc:26923|gfp:664|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#89|ssc:7976|tissue:Heart|well:A12                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#89 LCK 7#89 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 26923:fsc|Experimental Factor: 7976:ssc|Experimental Factor: 664:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_89_mod.bam LCK_7_89.cram bam cram     E MTAB 4617:LCK 7#89 0:125 1:125 A:53847121;C:51852010;G:47816940;T:57047962;N:23717 125 125     53847121 51852010 47816940 57047962 23717 ERX1497953   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.22382 0.21939 0.05208 0.05177 0.97952 0.97979 0.49483 0.59346 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4368 4368 ERR1427415 ERX1497947 ERS1183249 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#83 SAMEA4012139 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012139|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#83|broker name:ArrayExpress|common name:zebrafish|fsc:23855|gfp:97|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#83|ssc:7394|tissue:Heart|well:C11                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#83 LCK 7#83 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 23855:fsc|Experimental Factor: 7394:ssc|Experimental Factor: 97:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_83_mod.bam LCK_7_83.cram bam cram     E MTAB 4617:LCK 7#83 0:125 1:125 A:73686338;C:69380167;G:63301440;T:77949626;N:35429 125 125     73686338 69380167 63301440 77949626 35429 ERX1497947   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.1643 0.16094 0.06354 0.06267 0.98526 0.98581 0.60921 0.60841 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4369 4369 ERR1427414 ERX1497946 ERS1183248 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#82 SAMEA4012138 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012138|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#82|broker name:ArrayExpress|common name:zebrafish|fsc:27473|gfp:554|individual:2|pi:3|plate:7|sample name:E MTAB 4617:LCK 7#82|ssc:9625|tissue:Heart|well:B11                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#82 LCK 7#82 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 27473:fsc|Experimental Factor: 9625:ssc|Experimental Factor: 554:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_82_mod.bam LCK_7_82.cram bam cram     E MTAB 4617:LCK 7#82 0:125 1:125 A:132306808;C:126337107;G:118115874;T:139760194;N:65267 125 125     132306808 126337107 118115874 139760194 65267 ERX1497946   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.18655 0.18247 0.05663 0.05588 0.97916 0.97918 0.57019 0.56851 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4370 4370 ERR1427413 ERX1497945 ERS1183247 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#81 SAMEA4012137 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012137|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#81|broker name:ArrayExpress|common name:zebrafish|fsc:26381|gfp:492|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#81|ssc:6369|tissue:Heart|well:A11                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#81 LCK 7#81 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 26381:fsc|Experimental Factor: 6369:ssc|Experimental Factor: 492:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_81_mod.bam LCK_7_81.cram bam cram     E MTAB 4617:LCK 7#81 0:125 1:125 A:49752056;C:47569625;G:43787172;T:52848426;N:21471 125 125     49752056 47569625 43787172 52848426 21471 ERX1497945   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.18831 0.18533 0.05553 0.05564 0.98076 0.98147 0.55231 0.5582 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4377 4377 ERR1427406 ERX1497938 ERS1183240 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#75 SAMEA4012130 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012130|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#75|broker name:ArrayExpress|common name:zebrafish|fsc:29804|gfp:381|individual:2|pi:3|plate:7|sample name:E MTAB 4617:LCK 7#75|ssc:9855|tissue:Heart|well:C10                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#75 LCK 7#75 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 29804:fsc|Experimental Factor: 9855:ssc|Experimental Factor: 381:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_75_mod.bam LCK_7_75.cram bam cram     E MTAB 4617:LCK 7#75 0:125 1:125 A:215270392;C:173814423;G:161953517;T:222035470;N:96448 125 125     215270392 173814423 161953517 222035470 96448 ERX1497938   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.40731 0.4045 0.14845 0.14768 0.97908 0.97906 0.59339 0.61288 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4378 4378 ERR1427405 ERX1497937 ERS1183239 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#74 SAMEA4012129 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012129|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#74|broker name:ArrayExpress|common name:zebrafish|fsc:27947|gfp:352|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#74|ssc:7917|tissue:Heart|well:B10                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#74 LCK 7#74 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 27947:fsc|Experimental Factor: 7917:ssc|Experimental Factor: 352:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_74_mod.bam LCK_7_74.cram bam cram     E MTAB 4617:LCK 7#74 0:125 1:125 A:123931531;C:111767107;G:106439636;T:128665381;N:58095 125 125     123931531 111767107 106439636 128665381 58095 ERX1497937   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.24486 0.2405 0.06375 0.06316 0.97845 0.97938 0.55948 0.55443 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4379 4379 ERR1427404 ERX1497936 ERS1183238 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#73 SAMEA4012128 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012128|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#73|broker name:ArrayExpress|common name:zebrafish|fsc:27976|gfp:511|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#73|ssc:9269|tissue:Heart|well:A10                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#73 LCK 7#73 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 27976:fsc|Experimental Factor: 9269:ssc|Experimental Factor: 511:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_73_mod.bam LCK_7_73.cram bam cram     E MTAB 4617:LCK 7#73 0:125 1:125 A:47487658;C:44369011;G:41797745;T:49759850;N:22236 125 125     47487658 44369011 41797745 49759850 22236 ERX1497936   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.20054 0.19572 0.06216 0.06174 0.98141 0.98165 0.57621 0.56697 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4386 4386 ERR1427397 ERX1497929 ERS1183231 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#67 SAMEA4012121 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012121|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#67|broker name:ArrayExpress|common name:zebrafish|fsc:27129|gfp:522|individual:2|pi:3|plate:7|sample name:E MTAB 4617:LCK 7#67|ssc:7035|tissue:Heart|well:C9                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#67 LCK 7#67 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 27129:fsc|Experimental Factor: 7035:ssc|Experimental Factor: 522:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_67_mod.bam LCK_7_67.cram bam cram     E MTAB 4617:LCK 7#67 0:125 1:125 A:211181074;C:167361986;G:152479010;T:214248000;N:87930 125 125     211181074 167361986 152479010 214248000 87930 ERX1497929   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.35381 0.35317 0.14449 0.14491 0.97865 0.97897 0.57854 0.58021 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4387 4387 ERR1427396 ERX1497928 ERS1183230 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#66 SAMEA4012120 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012120|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#66|broker name:ArrayExpress|common name:zebrafish|fsc:23015|gfp:48|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#66|ssc:6562|tissue:Heart|well:B9                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#66 LCK 7#66 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 23015:fsc|Experimental Factor: 6562:ssc|Experimental Factor: 48:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_66_mod.bam LCK_7_66.cram bam cram     E MTAB 4617:LCK 7#66 0:125 1:125 A:122494933;C:109921862;G:103257549;T:125665684;N:56722 125 125     122494933 109921862 103257549 125665684 56722 ERX1497928   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.18714 0.18418 0.0608 0.06082 0.9839 0.98441 0.60081 0.59623 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4388 4388 ERR1427395 ERX1497927 ERS1183229 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#65 SAMEA4012119 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012119|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#65|broker name:ArrayExpress|common name:zebrafish|fsc:23857|gfp:308|individual:2|pi:4|plate:7|sample name:E MTAB 4617:LCK 7#65|ssc:4888|tissue:Heart|well:A9                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#65 LCK 7#65 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 23857:fsc|Experimental Factor: 4888:ssc|Experimental Factor: 308:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_65_mod.bam LCK_7_65.cram bam cram     E MTAB 4617:LCK 7#65 0:125 1:125 A:96259909;C:89965165;G:84222055;T:99868995;N:43376 125 125     96259909 89965165 84222055 99868995 43376 ERX1497927   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.25582 0.25073 0.07651 0.07583 0.98044 0.98106 0.67809 0.67977 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4395 4395 ERR1427388 ERX1497920 ERS1183222 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#59 SAMEA4012112 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012112|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#59|broker name:ArrayExpress|common name:zebrafish|fsc:20472|gfp:126|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#59|ssc:10300|tissue:Heart|well:C8                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#59 LCK 7#59 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 20472:fsc|Experimental Factor: 10300:ssc|Experimental Factor: 126:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_59_mod.bam LCK_7_59.cram bam cram     E MTAB 4617:LCK 7#59 0:125 1:125 A:134247255;C:121203898;G:112067297;T:140566781;N:62269 125 125     134247255 121203898 112067297 140566781 62269 ERX1497920   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.27548 0.27103 0.09818 0.09707 0.97861 0.97922 0.54371 0.57755 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4396 4396 ERR1427387 ERX1497919 ERS1183221 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#58 SAMEA4012111 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012111|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#58|broker name:ArrayExpress|common name:zebrafish|fsc:30361|gfp:242|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#58|ssc:7886|tissue:Heart|well:B8                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#58 LCK 7#58 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 30361:fsc|Experimental Factor: 7886:ssc|Experimental Factor: 242:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_58_mod.bam LCK_7_58.cram bam cram     E MTAB 4617:LCK 7#58 0:125 1:125 A:165043952;C:161634321;G:152303735;T:174314970;N:75022 125 125     165043952 161634321 152303735 174314970 75022 ERX1497919   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.16408 0.16208 0.06572 0.06486 0.97918 0.97922 0.52752 0.52567 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4397 4397 ERR1427386 ERX1497918 ERS1183220 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#57 SAMEA4012110 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012110|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#57|broker name:ArrayExpress|common name:zebrafish|fsc:30152|gfp:130|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#57|ssc:6428|tissue:Heart|well:A8                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#57 LCK 7#57 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 30152:fsc|Experimental Factor: 6428:ssc|Experimental Factor: 130:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_57_mod.bam LCK_7_57.cram bam cram     E MTAB 4617:LCK 7#57 0:125 1:125 A:81845074;C:82172065;G:76757417;T:87625766;N:38678 125 125     81845074 82172065 76757417 87625766 38678 ERX1497918   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.11381 0.11124 0.03217 0.03208 0.98253 0.98299 0.58282 0.58741 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4403 4403 ERR1427380 ERX1497912 ERS1183214 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#51 SAMEA4012104 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012104|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#51|broker name:ArrayExpress|common name:zebrafish|fsc:28503|gfp:536|individual:2|pi:3|plate:7|sample name:E MTAB 4617:LCK 7#51|ssc:5896|tissue:Heart|well:C7                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#51 LCK 7#51 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 28503:fsc|Experimental Factor: 5896:ssc|Experimental Factor: 536:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_51_mod.bam LCK_7_51.cram bam cram     E MTAB 4617:LCK 7#51 0:125 1:125 A:68083321;C:57560520;G:49834107;T:71348826;N:28226 125 125     68083321 57560520 49834107 71348826 28226 ERX1497912   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.22734 0.22491 0.09383 0.09424 0.98019 0.98127 0.60101 0.59084 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4404 4404 ERR1427379 ERX1497911 ERS1183213 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#50 SAMEA4012103 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012103|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#50|broker name:ArrayExpress|common name:zebrafish|fsc:27497|gfp:574|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#50|ssc:8308|tissue:Heart|well:B7                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#50 LCK 7#50 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 27497:fsc|Experimental Factor: 8308:ssc|Experimental Factor: 574:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_50_mod.bam LCK_7_50.cram bam cram     E MTAB 4617:LCK 7#50 0:125 1:125 A:200436684;C:191639110;G:173623845;T:213497904;N:94207 125 125     200436684 191639110 173623845 213497904 94207 ERX1497911   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.08784 0.08742 0.04628 0.04599 0.98784 0.98823 0.5655 0.56486 125 125 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4406 4406 ERR1427377 ERX1497909 ERS1183211 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#49 SAMEA4012101 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012101|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#49|broker name:ArrayExpress|common name:zebrafish|fsc:30443|gfp:456|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#49|ssc:8077|tissue:Heart|well:A7                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#49 LCK 7#49 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 30443:fsc|Experimental Factor: 8077:ssc|Experimental Factor: 456:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_49_mod.bam LCK_7_49.cram bam cram     E MTAB 4617:LCK 7#49 0:125 1:125 A:96840239;C:94376256;G:85197984;T:104185788;N:45483 125 125     96840239 94376256 85197984 104185788 45483 ERX1497909   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.17039 0.16705 0.05666 0.05595 0.98133 0.98196 0.59139 0.59279 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4412 4412 ERR1427371 ERX1497903 ERS1183205 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#43 SAMEA4012095 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012095|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#43|broker name:ArrayExpress|common name:zebrafish|fsc:21270|gfp:120|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#43|ssc:7066|tissue:Heart|well:C6                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#43 LCK 7#43 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 21270:fsc|Experimental Factor: 7066:ssc|Experimental Factor: 120:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_43_mod.bam LCK_7_43.cram bam cram     E MTAB 4617:LCK 7#43 0:125 1:125 A:95132366;C:87995738;G:81475905;T:100137372;N:45119 125 125     95132366 87995738 81475905 100137372 45119 ERX1497903   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.21518 0.21129 0.06702 0.06612 0.97887 0.97944 0.5799 0.57556 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4413 4413 ERR1427370 ERX1497902 ERS1183204 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#42 SAMEA4012094 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012094|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#42|broker name:ArrayExpress|common name:zebrafish|fsc:19274|gfp:88|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#42|ssc:6422|tissue:Heart|well:B6                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#42 LCK 7#42 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 19274:fsc|Experimental Factor: 6422:ssc|Experimental Factor: 88:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_42_mod.bam LCK_7_42.cram bam cram     E MTAB 4617:LCK 7#42 0:125 1:125 A:45015627;C:40505684;G:37787157;T:46787414;N:20618 125 125     45015627 40505684 37787157 46787414 20618 ERX1497902   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.14859 0.1471 0.0553 0.05579 0.98058 0.98151 0.57477 0.57968 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4414 4414 ERR1427369 ERX1497901 ERS1183203 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#41 SAMEA4012093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012093|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#41|broker name:ArrayExpress|common name:zebrafish|fsc:20292|gfp:198|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#41|ssc:6233|tissue:Heart|well:A6                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#41 LCK 7#41 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 20292:fsc|Experimental Factor: 6233:ssc|Experimental Factor: 198:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_41_mod.bam LCK_7_41.cram bam cram     E MTAB 4617:LCK 7#41 0:125 1:125 A:89502636;C:89074499;G:83078909;T:95568395;N:39311 125 125     89502636 89074499 83078909 95568395 39311 ERX1497901   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.09383 0.09131 0.02199 0.02189 0.98569 0.98577 0.58856 0.59531 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4421 4421 ERR1427362 ERX1497894 ERS1183196 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#35 SAMEA4012086 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012086|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#35|broker name:ArrayExpress|common name:zebrafish|fsc:26079|gfp:93|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#35|ssc:4930|tissue:Heart|well:C5                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#35 LCK 7#35 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 26079:fsc|Experimental Factor: 4930:ssc|Experimental Factor: 93:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_35_mod.bam LCK_7_35.cram bam cram     E MTAB 4617:LCK 7#35 0:125 1:125 A:139844227;C:137312069;G:126169914;T:149207606;N:69934 125 125     139844227 137312069 126169914 149207606 69934 ERX1497894   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.19648 0.19308 0.05501 0.05463 0.98149 0.982 0.60289 0.60804 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4422 4422 ERR1427361 ERX1497893 ERS1183195 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#34 SAMEA4012085 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012085|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#34|broker name:ArrayExpress|common name:zebrafish|fsc:25615|gfp:81|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#34|ssc:5934|tissue:Heart|well:B5                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#34 LCK 7#34 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 25615:fsc|Experimental Factor: 5934:ssc|Experimental Factor: 81:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_34_mod.bam LCK_7_34.cram bam cram     E MTAB 4617:LCK 7#34 0:125 1:125 A:134481938;C:127574886;G:118538403;T:142102568;N:61455 125 125     134481938 127574886 118538403 142102568 61455 ERX1497893   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.19982 0.1964 0.06657 0.0662 0.98092 0.98119 0.59089 0.58445 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4423 4423 ERR1427360 ERX1497892 ERS1183194 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#33 SAMEA4012084 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012084|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#33|broker name:ArrayExpress|common name:zebrafish|fsc:28221|gfp:414|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#33|ssc:5341|tissue:Heart|well:A5                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#33 LCK 7#33 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 28221:fsc|Experimental Factor: 5341:ssc|Experimental Factor: 414:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_33_mod.bam LCK_7_33.cram bam cram     E MTAB 4617:LCK 7#33 0:125 1:125 A:93220735;C:94390552;G:86770054;T:100705096;N:43313 125 125     93220735 94390552 86770054 100705096 43313 ERX1497892   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.09686 0.09522 0.02902 0.02873 0.98228 0.98279 0.54935 0.54646 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4427 4427 ERR1427356 ERX1497888 ERS1183190 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#3 SAMEA4012080 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012080|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#3|broker name:ArrayExpress|common name:zebrafish|fsc:25075|gfp:108|individual:2|pi:4|plate:7|sample name:E MTAB 4617:LCK 7#3|ssc:7682|tissue:Heart|well:C1                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#3 LCK 7#3 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 25075:fsc|Experimental Factor: 7682:ssc|Experimental Factor: 108:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_3_mod.bam LCK_7_3.cram bam cram     E MTAB 4617:LCK 7#3 0:125 1:125 A:58493174;C:54183075;G:50060440;T:61036959;N:28352 125 125     58493174 54183075 50060440 61036959 28352 ERX1497888   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.15762 0.1526 0.04924 0.04785 0.97906 0.97966 0.55641 0.55037 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4430 4430 ERR1427353 ERX1497885 ERS1183187 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#27 SAMEA4012077 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012077|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#27|broker name:ArrayExpress|common name:zebrafish|fsc:29359|gfp:456|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#27|ssc:10950|tissue:Heart|well:C4                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#27 LCK 7#27 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 29359:fsc|Experimental Factor: 10950:ssc|Experimental Factor: 456:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_27_mod.bam LCK_7_27.cram bam cram     E MTAB 4617:LCK 7#27 0:125 1:125 A:116175271;C:110956295;G:101584573;T:123371066;N:51045 125 125     116175271 110956295 101584573 123371066 51045 ERX1497885   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.25865 0.25265 0.08041 0.07902 0.97601 0.97595 0.55457 0.55357 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4431 4431 ERR1427352 ERX1497884 ERS1183186 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#26 SAMEA4012076 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012076|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#26|broker name:ArrayExpress|common name:zebrafish|fsc:25525|gfp:162|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#26|ssc:5861|tissue:Heart|well:B4                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#26 LCK 7#26 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 25525:fsc|Experimental Factor: 5861:ssc|Experimental Factor: 162:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_26_mod.bam LCK_7_26.cram bam cram     E MTAB 4617:LCK 7#26 0:125 1:125 A:84022783;C:79751329;G:73366671;T:88820379;N:40588 125 125     84022783 79751329 73366671 88820379 40588 ERX1497884   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.13334 0.13062 0.04098 0.04053 0.98405 0.98439 0.43923 0.56542 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4432 4432 ERR1427351 ERX1497883 ERS1183185 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#25 SAMEA4012075 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012075|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#25|broker name:ArrayExpress|common name:zebrafish|fsc:28284|gfp:515|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#25|ssc:8791|tissue:Heart|well:A4                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#25 LCK 7#25 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 28284:fsc|Experimental Factor: 8791:ssc|Experimental Factor: 515:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_25_mod.bam LCK_7_25.cram bam cram     E MTAB 4617:LCK 7#25 0:125 1:125 A:93291373;C:90572911;G:83617400;T:99965116;N:42450 125 125     93291373 90572911 83617400 99965116 42450 ERX1497883   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.22059 0.21595 0.06285 0.06239 0.97739 0.97755 0.60441 0.5941 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4438 4438 ERR1427345 ERX1497877 ERS1183179 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#2 SAMEA4012069 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012069|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#2|broker name:ArrayExpress|common name:zebrafish|fsc:26546|gfp:74|individual:2|pi:4|plate:7|sample name:E MTAB 4617:LCK 7#2|ssc:5884|tissue:Heart|well:B1                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#2 LCK 7#2 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 26546:fsc|Experimental Factor: 5884:ssc|Experimental Factor: 74:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_2_mod.bam LCK_7_2.cram bam cram     E MTAB 4617:LCK 7#2 0:125 1:125 A:50810642;C:45505266;G:42437381;T:52252338;N:22373 125 125     50810642 45505266 42437381 52252338 22373 ERX1497877   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.13878 0.13634 0.03454 0.03422 0.98179 0.98238 0.53282 0.54119 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4439 4439 ERR1427344 ERX1497876 ERS1183178 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#19 SAMEA4012068 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012068|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#19|broker name:ArrayExpress|common name:zebrafish|fsc:27939|gfp:269|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#19|ssc:7748|tissue:Heart|well:C3                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#19 LCK 7#19 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 27939:fsc|Experimental Factor: 7748:ssc|Experimental Factor: 269:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_19_mod.bam LCK_7_19.cram bam cram     E MTAB 4617:LCK 7#19 0:125 1:125 A:123448577;C:117648440;G:109679332;T:127799152;N:59249 125 125     123448577 117648440 109679332 127799152 59249 ERX1497876   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.20997 0.20449 0.04702 0.04606 0.98013 0.98068 0.58105 0.58018 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4440 4440 ERR1427343 ERX1497875 ERS1183177 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#18 SAMEA4012067 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012067|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#18|broker name:ArrayExpress|common name:zebrafish|fsc:23930|gfp:89|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#18|ssc:7002|tissue:Heart|well:B3                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#18 LCK 7#18 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 23930:fsc|Experimental Factor: 7002:ssc|Experimental Factor: 89:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_18_mod.bam LCK_7_18.cram bam cram     E MTAB 4617:LCK 7#18 0:125 1:125 A:116722795;C:108761302;G:102297772;T:120311653;N:53978 125 125     116722795 108761302 102297772 120311653 53978 ERX1497875   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.17035 0.16607 0.04165 0.04071 0.98275 0.98315 0.57334 0.56296 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4441 4441 ERR1427342 ERX1497874 ERS1183176 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#17 SAMEA4012066 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012066|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#17|broker name:ArrayExpress|common name:zebrafish|fsc:19157|gfp:158|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#17|ssc:7404|tissue:Heart|well:A3                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#17 LCK 7#17 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 19157:fsc|Experimental Factor: 7404:ssc|Experimental Factor: 158:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_17_mod.bam LCK_7_17.cram bam cram     E MTAB 4617:LCK 7#17 0:125 1:125 A:114273839;C:106761242;G:100217178;T:118680369;N:52122 125 125     114273839 106761242 100217178 118680369 52122 ERX1497874   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.26249 0.25596 0.06917 0.06842 0.9737 0.97425 0.59255 0.59411 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4447 4447 ERR1427336 ERX1497868 ERS1183170 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#11 SAMEA4012060 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012060|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#11|broker name:ArrayExpress|common name:zebrafish|fsc:23053|gfp:148|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#11|ssc:3985|tissue:Heart|well:C2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#11 LCK 7#11 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 23053:fsc|Experimental Factor: 3985:ssc|Experimental Factor: 148:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_11_mod.bam LCK_7_11.cram bam cram     E MTAB 4617:LCK 7#11 0:125 1:125 A:94603298;C:90252097;G:83046109;T:99899414;N:44332 125 125     94603298 90252097 83046109 99899414 44332 ERX1497868   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.24988 0.24291 0.07669 0.07453 0.97857 0.97901 0.52877 0.53451 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4448 4448 ERR1427335 ERX1497867 ERS1183169 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#10 SAMEA4012059 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012059|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#10|broker name:ArrayExpress|common name:zebrafish|fsc:26350|gfp:91|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#10|ssc:5717|tissue:Heart|well:B2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#10 LCK 7#10 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 26350:fsc|Experimental Factor: 5717:ssc|Experimental Factor: 91:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_10_mod.bam LCK_7_10.cram bam cram     E MTAB 4617:LCK 7#10 0:125 1:125 A:136048498;C:130651014;G:121379521;T:142822578;N:64889 125 125     136048498 130651014 121379521 142822578 64889 ERX1497867   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.14978 0.14551 0.04586 0.0445 0.98516 0.98559 0.55716 0.54592 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
4449 4449 ERR1427334 ERX1497866 ERS1183168 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#1 SAMEA4012058 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012058|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#1|broker name:ArrayExpress|common name:zebrafish|fsc:22006|gfp:487|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#1|ssc:6542|tissue:Heart|well:A1                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#1 LCK 7#1 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Heart:tissue|Experimental Factor: 22006:fsc|Experimental Factor: 6542:ssc|Experimental Factor: 487:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_1_mod.bam LCK_7_1.cram bam cram     E MTAB 4617:LCK 7#1 0:125 1:125 A:128250593;C:122748202;G:114418508;T:135400263;N:59934 125 125     128250593 122748202 114418508 135400263 59934 ERX1497866   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.15168 0.14994 0.07129 0.07092 0.98202 0.98163 0.61662 0.63065 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Heart Cardiovascular System
8065 8065 ERR035546 ERX013539 ERS017860 ERP000447 PRJEB2368 Sanger zebrafish sequencing E-MTAB-460 Other       Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Zebrafish adult heart SAMEA782570 Wellcome Sanger Institute ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782570|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult heart|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:heart|sample name:E MTAB 460:Zebrafish adult heart|sex:mixed                 Sanger zebrafish sequencing E MTAB 460 part2:5625 2 ZFheart 2 RNA 1523493 Sanger zebrafish sequencing Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was enriched for polyA+ RNA by 2 rounds of polyA pull down with magnetic beads and included a DNase treatment between the 2 rounds. RNA was chemically fragmented LiCl precipitated reverse transcribed with random primers a second strand synthesized and made into a standard Illumina library with a fragment size of 250 to 300 bp. Experimental Factor: ORGANISM PART:heart RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>2</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>85</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP000447 Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing ENA FIRST PUBLIC:2011 06 14|ENA LAST UPDATE:2018 11 16 5625_2.srf srf 4268641920.0 26679012.0 E MTAB 460 part2:5625 2.srf 0:76 1:8 2:76 A:1091431814;C:927546313;G:930574449;T:1098343870;N:7313378 76 8 76   1091431814 927546313 930574449 1098343870 7313378 ERX013539 ERS017860 ERA033503 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.89019 0.88267 0.09729 0.09648 0.75396 0.75682 0.49617 0.48086 76 76 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United Kingdom 2011-02-03 Adult Adult Heart Cardiovascular System
8071 8071 ERR023150 ERX009447 ERS017860 ERP000447 PRJEB2368 Sanger zebrafish sequencing E-MTAB-460 Other       Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Zebrafish adult heart SAMEA782570 Wellcome Sanger Institute ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782570|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult heart|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:heart|sample name:E MTAB 460:Zebrafish adult heart|sex:mixed                 Sanger zebrafish sequencing E MTAB 460:4191 7 RNA from Zebrafish adult heart Sanger zebrafish sequencing Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Experimental Factor: ORGANISM PART:heart RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP000447 Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing ENA FIRST PUBLIC:2011 02 03|ENA LAST UPDATE:2018 11 16 4191_7.srf srf 3679011648.0 24204024.0 E MTAB 460:4191 7.srf 0:76 1:76 A:1284614952;C:552903359;G:563080702;T:1273094378;N:5318257 76 76     1284614952 552903359 563080702 1273094378 5318257 ERX009447 ERS017860 ERA015648 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.85359 0.84739 0.30719 0.3063 0.82806 0.82686 0.52003 0.52279 76 76 B B biological fallback assumption illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2011-02-03 Adult Adult Heart Cardiovascular System
8073 8073 ERR023145 ERX009445 ERS017860 ERP000447 PRJEB2368 Sanger zebrafish sequencing E-MTAB-460 Other       Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Zebrafish adult heart SAMEA782570 Wellcome Sanger Institute ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782570|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult heart|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:heart|sample name:E MTAB 460:Zebrafish adult heart|sex:mixed                 Sanger zebrafish sequencing E MTAB 460:3212 7 RNA from Zebrafish adult heart Sanger zebrafish sequencing Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Experimental Factor: ORGANISM PART:heart RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP000447 Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing ENA FIRST PUBLIC:2011 02 03|ENA LAST UPDATE:2018 11 16 3212_7.srf srf 590858656.0 3887228.0 E MTAB 460:3212 7.srf 0:76 1:76 A:198026008;C:95340719;G:91816629;T:200078264;N:5597036 76 76     198026008 95340719 91816629 200078264 5597036 ERX009445 ERS017860 ERA015648 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.85463 0.85526 0.2737 0.27538 0.82189 0.82282 0.55114 0.5482 76 76 B B biological fallback assumption illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2011-02-03 Adult Adult Heart Cardiovascular System
10216 10216 ERR6501834 ERX6129007 ERS7415871 ERP131229 PRJEB46994 Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf E-MTAB-10860 Transcriptome Analysis This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts extracted and processed identically. RNA sequencing quality control and alignment was performed by the commercial company GENEWIZ. ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01   Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf Uninjured 3 SAMEA9691614 University Of Edinburgh ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691614|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Uninjured 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 6 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Uninjured 3|sex:not available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf E MTAB 10860:Uninjured 3 p Uninjured 3 p Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf Experimental Factor: injury:n1 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP131229 Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01 un-3_R1_001.fastq.gz un-3_R2_001.fastq.gz fastq fastq 18723567013.0 65061888.0 E MTAB 10860:un 3 R 0:143.87 1:143.91 A:4417527025;C:4932613578;G:4960694819;T:4412305366;N:426225 143 143     4417527025 4932613578 4960694819 4412305366 426225 ERX6129007 ERS7415871 ERA5680505 University Of Edinburgh|European Nucleotide Archive University Of Edinburgh|European Nucleotide Archive 2 0.96755 0.96744 0.18873 0.18936 0.72868 0.73235 0.632 0.6437 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United Kingdom 2021-10-01 Larval Larval Heart Cardiovascular System
10217 10217 ERR6501833 ERX6129006 ERS7415870 ERP131229 PRJEB46994 Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf E-MTAB-10860 Transcriptome Analysis This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts extracted and processed identically. RNA sequencing quality control and alignment was performed by the commercial company GENEWIZ. ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01   Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf Uninjured 2 SAMEA9691613 University Of Edinburgh ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691613|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Uninjured 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 5 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Uninjured 2|sex:not available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf E MTAB 10860:Uninjured 2 p Uninjured 2 p Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf Experimental Factor: injury:n1 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP131229 Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01 un-2_R1_001.fastq.gz un-2_R2_001.fastq.gz fastq fastq 16871358399.0 59064661.0 E MTAB 10860:un 2 R 0:142.77 1:142.88 A:4041490134;C:4380856328;G:4414614946;T:4033723935;N:673056 142 142     4041490134 4380856328 4414614946 4033723935 673056 ERX6129006 ERS7415870 ERA5680505 University Of Edinburgh|European Nucleotide Archive University Of Edinburgh|European Nucleotide Archive 2 0.96589 0.9656 0.15519 0.15447 0.70887 0.71062 0.60267 0.60735 150 147 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United Kingdom 2021-10-01 Larval Larval Heart Cardiovascular System
10218 10218 ERR6501832 ERX6129005 ERS7415869 ERP131229 PRJEB46994 Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf E-MTAB-10860 Transcriptome Analysis This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts extracted and processed identically. RNA sequencing quality control and alignment was performed by the commercial company GENEWIZ. ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01   Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf Uninjured 1 SAMEA9691612 University Of Edinburgh ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691612|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Uninjured 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 4 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Uninjured 1|sex:not available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf E MTAB 10860:Uninjured 1 p Uninjured 1 p Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf Experimental Factor: injury:n1 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP131229 Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01 un-1_R1_001.fastq.gz un-1_R2_001.fastq.gz fastq fastq 22029484310.0 76938931.0 E MTAB 10860:un 1 R 0:143.11 1:143.22 A:5407867825;C:5589867496;G:5636111894;T:5394805343;N:831752 143 143     5407867825 5589867496 5636111894 5394805343 831752 ERX6129005 ERS7415869 ERA5680505 University Of Edinburgh|European Nucleotide Archive University Of Edinburgh|European Nucleotide Archive 2 0.9602 0.95957 0.14282 0.14408 0.69649 0.69954 0.56712 0.56916 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United Kingdom 2021-10-01 Larval Larval Heart Cardiovascular System
10219 10219 ERR6501831 ERX6129004 ERS7415868 ERP131229 PRJEB46994 Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf E-MTAB-10860 Transcriptome Analysis This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts extracted and processed identically. RNA sequencing quality control and alignment was performed by the commercial company GENEWIZ. ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01   Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf Injured 3 SAMEA9691611 University Of Edinburgh ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691611|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Injured 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 3 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Injured 3|sex:not available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf E MTAB 10860:Injured 3 p Injured 3 p Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf Experimental Factor: injury:laser injury RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP131229 Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01 in-3_R1_001.fastq.gz in-3_R2_001.fastq.gz fastq fastq 7393087749.0 25640713.0 E MTAB 10860:in 3 R 0:144.14 1:144.20 A:1776335117;C:1913125420;G:1928181998;T:1775255039;N:190175 144 144     1776335117 1913125420 1928181998 1775255039 190175 ERX6129004 ERS7415868 ERA5680505 University Of Edinburgh|European Nucleotide Archive University Of Edinburgh|European Nucleotide Archive 2 0.96032 0.96001 0.15921 0.15882 0.71417 0.71869 0.59876 0.595 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United Kingdom 2021-10-01 Larval Larval Heart Cardiovascular System
10220 10220 ERR6501830 ERX6129003 ERS7415867 ERP131229 PRJEB46994 Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf E-MTAB-10860 Transcriptome Analysis This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts extracted and processed identically. RNA sequencing quality control and alignment was performed by the commercial company GENEWIZ. ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01   Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf Injured 2 SAMEA9691610 University Of Edinburgh ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691610|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Injured 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 2 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Injured 2|sex:not available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf E MTAB 10860:Injured 2 p Injured 2 p Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf Experimental Factor: injury:laser injury RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP131229 Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01 in-2_R1_001.fastq.gz in-2_R2_001.fastq.gz fastq fastq 9437508186.0 33059234.0 E MTAB 10860:in 2 R 0:142.70 1:142.77 A:2291798254;C:2421252733;G:2436117818;T:2288107030;N:232351 142 142     2291798254 2421252733 2436117818 2288107030 232351 ERX6129003 ERS7415867 ERA5680505 University Of Edinburgh|European Nucleotide Archive University Of Edinburgh|European Nucleotide Archive 2 0.96099 0.96042 0.14616 0.14802 0.70331 0.70674 0.53288 0.54459 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United Kingdom 2021-10-01 Larval Larval Heart Cardiovascular System
10221 10221 ERR6501829 ERX6129002 ERS7415866 ERP131229 PRJEB46994 Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf E-MTAB-10860 Transcriptome Analysis This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts extracted and processed identically. RNA sequencing quality control and alignment was performed by the commercial company GENEWIZ. ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01   Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf Injured 1 SAMEA9691609 University Of Edinburgh ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691609|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Injured 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 1 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Injured 1|sex:not available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf E MTAB 10860:Injured 1 p Injured 1 p Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf Experimental Factor: injury:laser injury RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP131229 Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01 in-1_R1_001.fastq.gz in-1_R2_001.fastq.gz fastq fastq 15465552702.0 54194727.0 E MTAB 10860:in 1 R 0:142.59 1:142.78 A:3807777989;C:3911855097;G:3946385823;T:3798685145;N:848648 142 142     3807777989 3911855097 3946385823 3798685145 848648 ERX6129002 ERS7415866 ERA5680505 University Of Edinburgh|European Nucleotide Archive University Of Edinburgh|European Nucleotide Archive 2 0.95721 0.95688 0.14331 0.14374 0.70262 0.70445 0.5114 0.52855 140 140 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United Kingdom 2021-10-01 Larval Larval Heart Cardiovascular System
11174 11174 ERR10180601 ERX9716167 ERS13447543 ERP140949 PRJEB56027 Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E-MTAB-12172 Transcriptome Analysis To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT cryaba / nrf2fh318/fh318 and cryaba / ;nrf2fh318/fh318 lines. ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24   Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. lens WT 2 SAMEA111349996 Vanderbilt Univiersity ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349996|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens WT 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:lens|sample name:E MTAB 12172:lens WT 2|sex:male                 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E MTAB 12172:lens WT 2 p lens WT 2 p Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140949 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24 5089-PP-2-CCATCCGC-AAGGCGTA_S01_L005_R1_001.fastq.gz 5089-PP-2-CCATCCGC-AAGGCGTA_S01_L005_R2_001.fastq.gz fastq fastq 16333543200.0 54445144.0 E MTAB 12172:5089 PP 2 CCATCCGC AAGGCGTA S01 L005 R 0:150 1:150 A:4190619330;C:3994540430;G:4078805527;T:4069157225;N:420688 150 150     4190619330 3994540430 4078805527 4069157225 420688 ERX9716167 ERS13447543 ERA17903080 Vanderbilt Univiersity|European Nucleotide Archive Vanderbilt Univiersity|European Nucleotide Archive 2 0.93689 0.9406 0.04209 0.04067 0.82698 0.82666 0.36086 0.43109 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11175 11175 ERR10180600 ERX9716166 ERS13447542 ERP140949 PRJEB56027 Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E-MTAB-12172 Transcriptome Analysis To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT cryaba / nrf2fh318/fh318 and cryaba / ;nrf2fh318/fh318 lines. ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24   Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. lens WT 1 SAMEA111349995 Vanderbilt Univiersity ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349995|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens WT 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:lens|sample name:E MTAB 12172:lens WT 1|sex:male                 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E MTAB 12172:lens WT 1 p lens WT 1 p Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140949 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24 5089-PP-1-ACAAGGCA-TCGCGCAA_S01_L005_R1_001.fastq.gz 5089-PP-1-ACAAGGCA-TCGCGCAA_S01_L005_R2_001.fastq.gz fastq fastq 15407010900.0 51356703.0 E MTAB 12172:5089 PP 1 ACAAGGCA TCGCGCAA S01 L005 R 0:150 1:150 A:3964097798;C:3754084768;G:3842793010;T:3845637263;N:398061 150 150     3964097798 3754084768 3842793010 3845637263 398061 ERX9716166 ERS13447542 ERA17903080 Vanderbilt Univiersity|European Nucleotide Archive Vanderbilt Univiersity|European Nucleotide Archive 2 0.94811 0.95125 0.04583 0.044 0.81844 0.81836 0.35718 0.43545 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11176 11176 ERR10180599 ERX9716165 ERS13447541 ERP140949 PRJEB56027 Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E-MTAB-12172 Transcriptome Analysis To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT cryaba / nrf2fh318/fh318 and cryaba / ;nrf2fh318/fh318 lines. ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24   Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. lens nrf2 mut 2 SAMEA111349994 Vanderbilt Univiersity ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349994|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens nrf2 mut 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:nrf2 mutant|organism part:lens|sample name:E MTAB 12172:lens nrf2 mut 2|sex:male                 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E MTAB 12172:lens nrf2 mut 2 p lens nrf2 mut 2 p Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. Experimental Factor: genotype:nrf2 mutant RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140949 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24 5089-PP-6-ACCAACAG-GTTTGCTC_S01_L005_R1_001.fastq.gz 5089-PP-6-ACCAACAG-GTTTGCTC_S01_L005_R2_001.fastq.gz fastq fastq 16160592300.0 53868641.0 E MTAB 12172:5089 PP 6 ACCAACAG GTTTGCTC S01 L005 R 0:150 1:150 A:4169968181;C:3949888212;G:4033930705;T:4006382078;N:423124 150 150     4169968181 3949888212 4033930705 4006382078 423124 ERX9716165 ERS13447541 ERA17903080 Vanderbilt Univiersity|European Nucleotide Archive Vanderbilt Univiersity|European Nucleotide Archive 2 0.96029 0.95994 0.04416 0.04259 0.82035 0.81982 0.36027 0.36601 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11177 11177 ERR10180598 ERX9716164 ERS13447540 ERP140949 PRJEB56027 Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E-MTAB-12172 Transcriptome Analysis To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT cryaba / nrf2fh318/fh318 and cryaba / ;nrf2fh318/fh318 lines. ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24   Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. lens nrf2 mut 1 SAMEA111349993 Vanderbilt Univiersity ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349993|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens nrf2 mut 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:nrf2 mutant|organism part:lens|sample name:E MTAB 12172:lens nrf2 mut 1|sex:male                 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E MTAB 12172:lens nrf2 mut 1 p lens nrf2 mut 1 p Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. Experimental Factor: genotype:nrf2 mutant RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140949 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24 5089-PP-5-GCACACAA-CTTGACGA_S01_L005_R1_001.fastq.gz 5089-PP-5-GCACACAA-CTTGACGA_S01_L005_R2_001.fastq.gz fastq fastq 13265052900.0 44216843.0 E MTAB 12172:5089 PP 5 GCACACAA CTTGACGA S01 L005 R 0:150 1:150 A:3416009346;C:3243776635;G:3305220346;T:3299701557;N:345016 150 150     3416009346 3243776635 3305220346 3299701557 345016 ERX9716164 ERS13447540 ERA17903080 Vanderbilt Univiersity|European Nucleotide Archive Vanderbilt Univiersity|European Nucleotide Archive 2 0.96137 0.95958 0.04396 0.04235 0.81505 0.8156 0.42582 0.44063 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11178 11178 ERR10180597 ERX9716163 ERS13447539 ERP140949 PRJEB56027 Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E-MTAB-12172 Transcriptome Analysis To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT cryaba / nrf2fh318/fh318 and cryaba / ;nrf2fh318/fh318 lines. ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24   Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. lens abanrf2 mut 2 SAMEA111349992 Vanderbilt Univiersity ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349992|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens abanrf2 mut 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout; nrf2 double mutant|organism part:lens|sample name:E MTAB 12172:lens abanrf2 mut 2|sex:male                 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E MTAB 12172:lens abanrf2 mut 2 p lens abanrf2 mut 2 p Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. Experimental Factor: genotype:cryaba knockout; nrf2 double mutant RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140949 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24 5089-PP-8-AACACCAC-GGTGTGAG_S01_L005_R1_001.fastq.gz 5089-PP-8-AACACCAC-GGTGTGAG_S01_L005_R2_001.fastq.gz fastq fastq 15388634400.0 51295448.0 E MTAB 12172:5089 PP 8 AACACCAC GGTGTGAG S01 L005 R 0:150 1:150 A:3958631492;C:3788327811;G:3838374812;T:3802892334;N:407951 150 150     3958631492 3788327811 3838374812 3802892334 407951 ERX9716163 ERS13447539 ERA17903080 Vanderbilt Univiersity|European Nucleotide Archive Vanderbilt Univiersity|European Nucleotide Archive 2 0.95795 0.95848 0.03631 0.0352 0.82686 0.82702 0.44398 0.43981 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11179 11179 ERR10180596 ERX9716162 ERS13447538 ERP140949 PRJEB56027 Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E-MTAB-12172 Transcriptome Analysis To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT cryaba / nrf2fh318/fh318 and cryaba / ;nrf2fh318/fh318 lines. ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24   Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. lens abanrf2 mut 1 SAMEA111349991 Vanderbilt Univiersity ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349991|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens abanrf2 mut 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout; nrf2 double mutant|organism part:lens|sample name:E MTAB 12172:lens abanrf2 mut 1|sex:male                 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E MTAB 12172:lens abanrf2 mut 1 p lens abanrf2 mut 1 p Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. Experimental Factor: genotype:cryaba knockout; nrf2 double mutant RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140949 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24 5089-PP-7-ATGTTCCT-TCAGCGCC_S01_L005_R1_001.fastq.gz 5089-PP-7-ATGTTCCT-TCAGCGCC_S01_L005_R2_001.fastq.gz fastq fastq 15994173600.0 53313912.0 E MTAB 12172:5089 PP 7 ATGTTCCT TCAGCGCC S01 L005 R 0:150 1:150 A:4099988245;C:3917478063;G:3992545834;T:3983743906;N:417552 150 150     4099988245 3917478063 3992545834 3983743906 417552 ERX9716162 ERS13447538 ERA17903080 Vanderbilt Univiersity|European Nucleotide Archive Vanderbilt Univiersity|European Nucleotide Archive 2 0.96127 0.95941 0.04117 0.03964 0.82047 0.82057 0.38606 0.37713 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11180 11180 ERR10180595 ERX9716161 ERS13447537 ERP140949 PRJEB56027 Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E-MTAB-12172 Transcriptome Analysis To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT cryaba / nrf2fh318/fh318 and cryaba / ;nrf2fh318/fh318 lines. ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24   Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. lens abaKO 2 SAMEA111349990 Vanderbilt Univiersity ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349990|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens abaKO 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout|organism part:lens|sample name:E MTAB 12172:lens abaKO 2|sex:male                 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E MTAB 12172:lens abaKO 2 p lens abaKO 2 p Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. Experimental Factor: genotype:cryaba knockout RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140949 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24 5089-PP-4-TCGCGCAA-ACAAGGCA_S01_L005_R1_001.fastq.gz 5089-PP-4-TCGCGCAA-ACAAGGCA_S01_L005_R2_001.fastq.gz fastq fastq 17799042900.0 59330143.0 E MTAB 12172:5089 PP 4 TCGCGCAA ACAAGGCA S01 L005 R 0:150 1:150 A:4545266681;C:4379648812;G:4457651334;T:4416025472;N:450601 150 150     4545266681 4379648812 4457651334 4416025472 450601 ERX9716161 ERS13447537 ERA17903080 Vanderbilt Univiersity|European Nucleotide Archive Vanderbilt Univiersity|European Nucleotide Archive 2 0.8747 0.87804 0.03407 0.03304 0.83999 0.84047 0.41026 0.42746 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11181 11181 ERR10180594 ERX9716160 ERS13447536 ERP140949 PRJEB56027 Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E-MTAB-12172 Transcriptome Analysis To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT cryaba / nrf2fh318/fh318 and cryaba / ;nrf2fh318/fh318 lines. ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24   Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. lens abaKO 1 SAMEA111349989 Vanderbilt Univiersity ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349989|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens abaKO 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout|organism part:lens|sample name:E MTAB 12172:lens abaKO 1|sex:male                 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E MTAB 12172:lens abaKO 1 p lens abaKO 1 p Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. Experimental Factor: genotype:cryaba knockout RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140949 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24 5089-PP-3-AAGGCGTA-CCATCCGC_S01_L005_R1_001.fastq.gz 5089-PP-3-AAGGCGTA-CCATCCGC_S01_L005_R2_001.fastq.gz fastq fastq 18850381500.0 62834605.0 E MTAB 12172:5089 PP 3 AAGGCGTA CCATCCGC S01 L005 R 0:150 1:150 A:4831021904;C:4613611754;G:4712103573;T:4693153324;N:490945 150 150     4831021904 4613611754 4712103573 4693153324 490945 ERX9716160 ERS13447536 ERA17903080 Vanderbilt Univiersity|European Nucleotide Archive Vanderbilt Univiersity|European Nucleotide Archive 2 0.94079 0.94389 0.04169 0.04008 0.82367 0.82524 0.4379 0.43771 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11182 11182 ERR10180593 ERX9716159 ERS13447535 ERP140949 PRJEB56027 Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E-MTAB-12172 Transcriptome Analysis To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT cryaba / nrf2fh318/fh318 and cryaba / ;nrf2fh318/fh318 lines. ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24   Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. heart WT 2 SAMEA111349988 Vanderbilt Univiersity ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349988|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart WT 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:heart|sample name:E MTAB 12172:heart WT 2|sex:male                 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E MTAB 12172:heart WT 2 p heart WT 2 p Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140949 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24 5539-JP-2-GATATGAA-TACGGCAG_S1_L001_R1_001.fastq.gz 5539-JP-2-GATATGAA-TACGGCAG_S1_L001_R2_001.fastq.gz fastq fastq 14304623100.0 47682077.0 E MTAB 12172:5539 JP 2 GATATGAA TACGGCAG S1 L001 R 0:150 1:150 A:3881337642;C:3260590900;G:3395614407;T:3766879544;N:200607 150 150     3881337642 3260590900 3395614407 3766879544 200607 ERX9716159 ERS13447535 ERA17903080 Vanderbilt Univiersity|European Nucleotide Archive Vanderbilt Univiersity|European Nucleotide Archive 2 0.94254 0.94698 0.05301 0.05137 0.77502 0.77352 0.50073 0.50274 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11183 11183 ERR10180592 ERX9716158 ERS13447534 ERP140949 PRJEB56027 Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E-MTAB-12172 Transcriptome Analysis To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT cryaba / nrf2fh318/fh318 and cryaba / ;nrf2fh318/fh318 lines. ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24   Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. heart WT 1 SAMEA111349987 Vanderbilt Univiersity ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349987|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart WT 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:heart|sample name:E MTAB 12172:heart WT 1|sex:male                 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E MTAB 12172:heart WT 1 p heart WT 1 p Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140949 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24 5539-JP-1-GTCCGATC-GCCAATCC_S1_L001_R1_001.fastq.gz 5539-JP-1-GTCCGATC-GCCAATCC_S1_L001_R2_001.fastq.gz fastq fastq 19185453300.0 63951511.0 E MTAB 12172:5539 JP 1 GTCCGATC GCCAATCC S1 L001 R 0:150 1:150 A:5172411335;C:4401564793;G:4571457514;T:5039775881;N:243777 150 150     5172411335 4401564793 4571457514 5039775881 243777 ERX9716158 ERS13447534 ERA17903080 Vanderbilt Univiersity|European Nucleotide Archive Vanderbilt Univiersity|European Nucleotide Archive 2 0.94765 0.95188 0.0548 0.05291 0.75986 0.76015 0.49801 0.49914 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11184 11184 ERR10180591 ERX9716157 ERS13447533 ERP140949 PRJEB56027 Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E-MTAB-12172 Transcriptome Analysis To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT cryaba / nrf2fh318/fh318 and cryaba / ;nrf2fh318/fh318 lines. ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24   Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. heart nrf2 mut 2 SAMEA111349986 Vanderbilt Univiersity ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349986|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart nrf2 mut 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:nrf2 mutant|organism part:heart|sample name:E MTAB 12172:heart nrf2 mut 2|sex:male                 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E MTAB 12172:heart nrf2 mut 2 p heart nrf2 mut 2 p Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. Experimental Factor: genotype:nrf2 mutant RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140949 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24 5539-JP-6-CCTTTCAC-TCTTGTTT_S1_L001_R1_001.fastq.gz 5539-JP-6-CCTTTCAC-TCTTGTTT_S1_L001_R2_001.fastq.gz fastq fastq 15506772300.0 51689241.0 E MTAB 12172:5539 JP 6 CCTTTCAC TCTTGTTT S1 L001 R 0:150 1:150 A:4206068868;C:3553449100;G:3659363790;T:4087684595;N:205947 150 150     4206068868 3553449100 3659363790 4087684595 205947 ERX9716157 ERS13447533 ERA17903080 Vanderbilt Univiersity|European Nucleotide Archive Vanderbilt Univiersity|European Nucleotide Archive 2 0.94875 0.95145 0.05898 0.05611 0.77254 0.77293 0.43478 0.41873 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11185 11185 ERR10180590 ERX9716156 ERS13447532 ERP140949 PRJEB56027 Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E-MTAB-12172 Transcriptome Analysis To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT cryaba / nrf2fh318/fh318 and cryaba / ;nrf2fh318/fh318 lines. ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24   Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. heart nrf2 mut 1 SAMEA111349985 Vanderbilt Univiersity ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349985|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart nrf2 mut 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:nrf2 mutant|organism part:heart|sample name:E MTAB 12172:heart nrf2 mut 1|sex:male                 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E MTAB 12172:heart nrf2 mut 1 p heart nrf2 mut 1 p Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. Experimental Factor: genotype:nrf2 mutant RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140949 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24 5539-JP-5-CACTAGAC-TGAGGACT_S1_L001_R1_001.fastq.gz 5539-JP-5-CACTAGAC-TGAGGACT_S1_L001_R2_001.fastq.gz fastq fastq 21738824700.0 72462749.0 E MTAB 12172:5539 JP 5 CACTAGAC TGAGGACT S1 L001 R 0:150 1:150 A:5871744282;C:5014617409;G:5151654454;T:5700519276;N:289279 150 150     5871744282 5014617409 5151654454 5700519276 289279 ERX9716156 ERS13447532 ERA17903080 Vanderbilt Univiersity|European Nucleotide Archive Vanderbilt Univiersity|European Nucleotide Archive 2 0.95074 0.95283 0.05595 0.05426 0.77193 0.77163 0.43329 0.49376 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11186 11186 ERR10180589 ERX9716155 ERS13447531 ERP140949 PRJEB56027 Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E-MTAB-12172 Transcriptome Analysis To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT cryaba / nrf2fh318/fh318 and cryaba / ;nrf2fh318/fh318 lines. ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24   Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. heart abanrf2 mut 2 SAMEA111349984 Vanderbilt Univiersity ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349984|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart abanrf2 mut 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout; nrf2 double mutant|organism part:heart|sample name:E MTAB 12172:heart abanrf2 mut 2|sex:male                 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E MTAB 12172:heart abanrf2 mut 2 p heart abanrf2 mut 2 p Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. Experimental Factor: genotype:cryaba knockout; nrf2 double mutant RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140949 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24 5539-JP-8-TACGGCAG-GATATGAA_S1_L001_R1_001.fastq.gz 5539-JP-8-TACGGCAG-GATATGAA_S1_L001_R2_001.fastq.gz fastq fastq 17223550800.0 57411836.0 E MTAB 12172:5539 JP 8 TACGGCAG GATATGAA S1 L001 R 0:150 1:150 A:4719158105;C:3846804288;G:4048574589;T:4608706331;N:307487 150 150     4719158105 3846804288 4048574589 4608706331 307487 ERX9716155 ERS13447531 ERA17903080 Vanderbilt Univiersity|European Nucleotide Archive Vanderbilt Univiersity|European Nucleotide Archive 2 0.93762 0.93789 0.0641 0.05916 0.77171 0.77465 0.50708 0.52073 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11187 11187 ERR10180588 ERX9716154 ERS13447530 ERP140949 PRJEB56027 Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E-MTAB-12172 Transcriptome Analysis To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT cryaba / nrf2fh318/fh318 and cryaba / ;nrf2fh318/fh318 lines. ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24   Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. heart abanrf2 mut 1 SAMEA111349983 Vanderbilt Univiersity ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349983|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart abanrf2 mut 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout; nrf2 double mutant|organism part:heart|sample name:E MTAB 12172:heart abanrf2 mut 1|sex:male                 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E MTAB 12172:heart abanrf2 mut 1 p heart abanrf2 mut 1 p Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. Experimental Factor: genotype:cryaba knockout; nrf2 double mutant RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140949 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24 5539-JP-7-GCCAATCC-GTCCGATC_S1_L001_R1_001.fastq.gz 5539-JP-7-GCCAATCC-GTCCGATC_S1_L001_R2_001.fastq.gz fastq fastq 14585545800.0 48618486.0 E MTAB 12172:5539 JP 7 GCCAATCC GTCCGATC S1 L001 R 0:150 1:150 A:3991503126;C:3300292702;G:3398962745;T:3894599059;N:188168 150 150     3991503126 3300292702 3398962745 3894599059 188168 ERX9716154 ERS13447530 ERA17903080 Vanderbilt Univiersity|European Nucleotide Archive Vanderbilt Univiersity|European Nucleotide Archive 2 0.9375 0.94022 0.06736 0.06462 0.76445 0.76495 0.50218 0.51223 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11188 11188 ERR10180587 ERX9716153 ERS13447529 ERP140949 PRJEB56027 Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E-MTAB-12172 Transcriptome Analysis To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT cryaba / nrf2fh318/fh318 and cryaba / ;nrf2fh318/fh318 lines. ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24   Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. heart abaKO 2 SAMEA111349982 Vanderbilt Univiersity ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349982|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart abaKO 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout|organism part:heart|sample name:E MTAB 12172:heart abaKO 2|sex:male                 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E MTAB 12172:heart abaKO 2 p heart abaKO 2 p Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. Experimental Factor: genotype:cryaba knockout RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140949 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24 5539-JP-4-TGTGTCAG-CACCTGTA_S1_L001_R1_001.fastq.gz 5539-JP-4-TGTGTCAG-CACCTGTA_S1_L001_R2_001.fastq.gz fastq fastq 16499634000.0 54998780.0 E MTAB 12172:5539 JP 4 TGTGTCAG CACCTGTA S1 L001 R 0:150 1:150 A:4448248023;C:3776948921;G:3924285767;T:4349924059;N:227230 150 150     4448248023 3776948921 3924285767 4349924059 227230 ERX9716153 ERS13447529 ERA17903080 Vanderbilt Univiersity|European Nucleotide Archive Vanderbilt Univiersity|European Nucleotide Archive 2 0.92566 0.92887 0.05292 0.05145 0.76741 0.76759 0.44001 0.44327 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2022-09-24 Adult Adult Heart Cardiovascular System
11189 11189 ERR10180586 ERX9716152 ERS13447528 ERP140949 PRJEB56027 Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E-MTAB-12172 Transcriptome Analysis To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT cryaba / nrf2fh318/fh318 and cryaba / ;nrf2fh318/fh318 lines. ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24   Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. heart abaKO 1 SAMEA111349981 Vanderbilt Univiersity ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349981|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart abaKO 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout|organism part:heart|sample name:E MTAB 12172:heart abaKO 1|sex:male                 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress E MTAB 12172:heart abaKO 1 p heart abaKO 1 p Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples. Experimental Factor: genotype:cryaba knockout RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140949 Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24 5539-JP-3-AGTCAGGT-GTAACCAC_S1_L001_R1_001.fastq.gz 5539-JP-3-AGTCAGGT-GTAACCAC_S1_L001_R2_001.fastq.gz fastq fastq 23723109000.0 79077030.0 E MTAB 12172:5539 JP 3 AGTCAGGT GTAACCAC S1 L001 R 0:150 1:150 A:6432327752;C:5406026214;G:5617874748;T:6266589522;N:290764 150 150     6432327752 5406026214 5617874748 6266589522 290764 ERX9716152 ERS13447528 ERA17903080 Vanderbilt Univiersity|European Nucleotide Archive Vanderbilt Univiersity|European Nucleotide Archive 2 0.94728 0.95029 0.05332 0.05201 0.76646 0.76838 0.50604 0.50579 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2022-09-24 Adult Adult Heart Cardiovascular System
15017 15017 ERR12352459 ERX11729321 ERS17282126 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Trpc6a KO sham 3 SAMEA114857167 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857167|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Trpc6a KO sham 3|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Trpc6a knockout|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:sham operated|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Trpc6a KO sham 3|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Trpc6a KO sham 3 p Trpc6a KO sham 3 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 3-Trpc6-KO-sham_R1_001.fastq.gz 3-Trpc6-KO-sham_R2_001.fastq.gz fastq fastq 9486677705.0 33558571.0 E MTAB 13603:3 Trpc6 KO sham R 0:141.09 1:141.60 A:2537673665;C:2192877777;G:2224713939;T:2525303945;N:6108379 141 141     2537673665 2192877777 2224713939 2525303945 6108379 ERX11729321 ERS17282126 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.95729 0.95618 0.07289 0.07124 0.7725 0.77481 0.52646 0.53221 149 150 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
15018 15018 ERR12352449 ERX11729311 ERS17282116 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Control 7dpa 1 SAMEA114857157 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857157|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Control 7dpa 1|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:cardiac resection|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Control 7dpa 1|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Control 7dpa 1 p Control 7dpa 1 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 4-Control-7dpa_R2_001.fastq.gz 4-Control-7dpa_R1_001.fastq.gz fastq fastq 6795430724.0 23938740.0 E MTAB 13603:4 Control 7dpa R 0:141.55 1:142.32 A:1815845541;C:1567718020;G:1597570908;T:1808008628;N:6287627 141 142     1815845541 1567718020 1597570908 1808008628 6287627 ERX11729311 ERS17282116 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.94648 0.94563 0.09062 0.08917 0.75087 0.75333 0.52273 0.51959 149 150 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
15019 15019 ERR12352452 ERX11729314 ERS17282119 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Control sham 1 SAMEA114857160 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857160|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Control sham 1|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:sham operated|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Control sham 1|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Control sham 1 p Control sham 1 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 1-Control-sham_R1_001.fastq.gz 1-Control-sham_R2_001.fastq.gz fastq fastq 15636676800.0 52122256.0 E MTAB 13603:1 Control sham R 0:150 1:150 A:4263031098;C:3519985187;G:3706349796;T:4147090133;N:220586 150 150     4263031098 3519985187 3706349796 4147090133 220586 ERX11729314 ERS17282119 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.94648 0.94897 0.06005 0.05942 0.76712 0.76822 0.51256 0.50643 150 150 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
15020 15020 ERR12352451 ERX11729313 ERS17282118 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Control 7dpa 3 SAMEA114857159 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857159|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Control 7dpa 3|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:cardiac resection|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Control 7dpa 3|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Control 7dpa 3 p Control 7dpa 3 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 6-Control-7dpa_R1_001.fastq.gz 6-Control-7dpa_R2_001.fastq.gz fastq fastq 8220300600.0 27401002.0 E MTAB 13603:6 Control 7dpa R 0:150 1:150 A:2242736911;C:1858506669;G:1911004513;T:2207938253;N:114254 150 150     2242736911 1858506669 1911004513 2207938253 114254 ERX11729313 ERS17282118 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.94374 0.94281 0.07308 0.07247 0.74028 0.7418 0.50319 0.50503 150 150 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
15021 15021 ERR12352457 ERX11729319 ERS17282124 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Trpc6a KO sham 1 SAMEA114857165 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857165|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Trpc6a KO sham 1|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Trpc6a knockout|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:sham operated|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Trpc6a KO sham 1|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Trpc6a KO sham 1 p Trpc6a KO sham 1 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 1-Trpc6-KO-sham_R1_001.fastq.gz 1-Trpc6-KO-sham_R2_001.fastq.gz fastq fastq 16463891400.0 54879638.0 E MTAB 13603:1 Trpc6 KO sham R 0:150 1:150 A:4481016793;C:3727761629;G:3905685351;T:4349193797;N:233830 150 150     4481016793 3727761629 3905685351 4349193797 233830 ERX11729319 ERS17282124 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.95234 0.95051 0.05908 0.05789 0.77477 0.77605 0.49876 0.50128 150 150 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
15022 15022 ERR12352458 ERX11729320 ERS17282125 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Trpc6a KO sham 2 SAMEA114857166 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857166|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Trpc6a KO sham 2|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Trpc6a knockout|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:sham operated|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Trpc6a KO sham 2|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Trpc6a KO sham 2 p Trpc6a KO sham 2 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 2-Trpc6-KO-sham_R1_001.fastq.gz 2-Trpc6-KO-sham_R2_001.fastq.gz fastq fastq 10449824700.0 34832749.0 E MTAB 13603:2 Trpc6 KO sham R 0:150 1:150 A:2842222574;C:2368784549;G:2449245548;T:2789428695;N:143334 150 150     2842222574 2368784549 2449245548 2789428695 143334 ERX11729320 ERS17282125 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.9539 0.95284 0.05851 0.05781 0.77425 0.77656 0.50514 0.50462 150 150 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
15023 15023 ERR12352453 ERX11729315 ERS17282120 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Control sham 2 SAMEA114857161 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857161|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Control sham 2|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:sham operated|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Control sham 2|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Control sham 2 p Control sham 2 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 2-Control-sham_R1_001.fastq.gz 2-Control-sham_R2_001.fastq.gz fastq fastq 13714149300.0 45713831.0 E MTAB 13603:2 Control sham R 0:150 1:150 A:3744799859;C:3102314317;G:3246683965;T:3620157056;N:194103 150 150     3744799859 3102314317 3246683965 3620157056 194103 ERX11729315 ERS17282120 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.94672 0.94688 0.05944 0.05917 0.76654 0.76773 0.51792 0.51959 150 150 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
15024 15024 ERR12352450 ERX11729312 ERS17282117 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Control 7dpa 2 SAMEA114857158 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857158|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Control 7dpa 2|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:cardiac resection|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Control 7dpa 2|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Control 7dpa 2 p Control 7dpa 2 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 5-Control-7dpa_R1_001.fastq.gz 5-Control-7dpa_R2_001.fastq.gz fastq fastq 9830629200.0 32768764.0 E MTAB 13603:5 Control 7dpa R 0:150 1:150 A:2655376287;C:2237942590;G:2372252275;T:2564920802;N:137246 150 150     2655376287 2237942590 2372252275 2564920802 137246 ERX11729312 ERS17282117 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.94476 0.94389 0.06625 0.06506 0.74197 0.7441 0.50589 0.50685 150 150 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
15025 15025 ERR12352454 ERX11729316 ERS17282121 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Trpc6a KO 7dpa 1 SAMEA114857162 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857162|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Trpc6a KO 7dpa 1|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Trpc6a knockout|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:cardiac resection|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Trpc6a KO 7dpa 1|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Trpc6a KO 7dpa 1 p Trpc6a KO 7dpa 1 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 4-Trpc6-KO-7dpa_R2_001.fastq.gz 4-Trpc6-KO-7dpa_R1_001.fastq.gz fastq fastq 5379338700.0 17931129.0 E MTAB 13603:4 Trpc6 KO 7dpa R 0:150 1:150 A:1451310854;C:1236467303;G:1283161720;T:1408322640;N:76183 150 150     1451310854 1236467303 1283161720 1408322640 76183 ERX11729316 ERS17282121 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.94369 0.94789 0.06027 0.06036 0.74647 0.74649 0.4767 0.50107 150 150 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
15026 15026 ERR12352455 ERX11729317 ERS17282122 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Trpc6a KO 7dpa 2 SAMEA114857163 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857163|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Trpc6a KO 7dpa 2|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Trpc6a knockout|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:cardiac resection|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Trpc6a KO 7dpa 2|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Trpc6a KO 7dpa 2 p Trpc6a KO 7dpa 2 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 5-Trpc6-KO-7dpa_R2_001.fastq.gz 5-Trpc6-KO-7dpa_R1_001.fastq.gz fastq fastq 14033980200.0 46779934.0 E MTAB 13603:5 Trpc6 KO 7dpa R 0:150 1:150 A:3810908166;C:3197374649;G:3343702230;T:3681798453;N:196702 150 150     3810908166 3197374649 3343702230 3681798453 196702 ERX11729317 ERS17282122 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.94801 0.94661 0.06342 0.06201 0.74834 0.75207 0.50789 0.5027 150 150 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
15027 15027 ERR12352456 ERX11729318 ERS17282123 ERP155844 PRJEB70944 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E-MTAB-13603 Transcriptome Analysis Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20   Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR Trpc6a KO 7dpa 3 SAMEA114857164 Institut de Génomique Fonctionnelle ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857164|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Trpc6a KO 7dpa 3|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Trpc6a knockout|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:cardiac resection|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Trpc6a KO 7dpa 3|scientific name:Danio rerio|sex:mix of males and females|strain:AB                 The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch E MTAB 13603:Trpc6a KO 7dpa 3 p Trpc6a KO 7dpa 3 p The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP155844 Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 6-Trpc6-KO-7dpa_R2_001.fastq.gz 6-Trpc6-KO-7dpa_R1_001.fastq.gz fastq fastq 10056041651.0 35562752.0 E MTAB 13603:6 Trpc6 KO 7dpa R 0:141.00 1:141.77 A:2670755890;C:2335065805;G:2381199297;T:2659552078;N:9468581 141 141     2670755890 2335065805 2381199297 2659552078 9468581 ERX11729318 ERS17282123 ERA27710226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.95324 0.9515 0.07632 0.07479 0.75597 0.75787 0.51981 0.52087 113 113 B B biological fallback assumption illumina novaseq_era 3prime poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-20 Adult Adult Heart Cardiovascular System
30708 30708 SRR28329751 SRX23938186 SRS20741667 SRP494974 PRJNA1087264 Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression GSE261479 Transcriptome Analysis Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods: Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 µM were collected for RNA seq.   pubmed:40053597   DAPT 3 GSM8144970   source name:hearts|tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DAPT|geo loc name:missing|collection date:missing DAPT 3 Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix between treatment samples and wild type samples. hearts 60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 μM to 96 hpf. 1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer’s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h. tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DAPT GSM8144970 GSM8144970: DAPT 3; Danio rerio; RNA Seq GSM8144970 r1 GSM8144970 1 1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP494974     DAPT_3_1.fq.gz DAPT_3_2.fq.gz fastq fastq 6899234400.0 34496172.0 GSM8144970 r1 0:100 1:100 A:1864675679;C:1564709308;G:1588106892;T:1881742521;N:0 100 100     1864675679 1564709308 1588106892 1881742521 0 SRX23938186 SRS20741667 SRA1823438 Institute of genetics, Zhejiang University Institute of genetics, Zhejiang University 2 0.93368 0.93504 0.09899 0.09916 0.67174 0.67095 0.51572 0.5101 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-03-13 Larval Larval Heart Cardiovascular System
30709 30709 SRR28329752 SRX23938185 SRS20741666 SRP494974 PRJNA1087264 Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression GSE261479 Transcriptome Analysis Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods: Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 µM were collected for RNA seq.   pubmed:40053597   DAPT 2 GSM8144969   source name:hearts|tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DAPT|geo loc name:missing|collection date:missing DAPT 2 Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix between treatment samples and wild type samples. hearts 60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 μM to 96 hpf. 1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer’s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h. tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DAPT GSM8144969 GSM8144969: DAPT 2; Danio rerio; RNA Seq GSM8144969 r1 GSM8144969 1 1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP494974     DAPT_2_1.fq.gz DAPT_2_2.fq.gz fastq fastq 6920695600.0 34603478.0 GSM8144969 r1 0:100 1:100 A:1880782056;C:1560368169;G:1581248339;T:1898297036;N:0 100 100     1880782056 1560368169 1581248339 1898297036 0 SRX23938185 SRS20741666 SRA1823438 Institute of genetics, Zhejiang University Institute of genetics, Zhejiang University 2 0.93355 0.93357 0.10276 0.10282 0.67363 0.67361 0.51703 0.52041 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-03-13 Larval Larval Heart Cardiovascular System
30710 30710 SRR28329753 SRX23938184 SRS20741665 SRP494974 PRJNA1087264 Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression GSE261479 Transcriptome Analysis Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods: Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 µM were collected for RNA seq.   pubmed:40053597   DAPT 1 GSM8144968   source name:hearts|tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DAPT|geo loc name:missing|collection date:missing DAPT 1 Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix between treatment samples and wild type samples. hearts 60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 μM to 96 hpf. 1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer’s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h. tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DAPT GSM8144968 GSM8144968: DAPT 1; Danio rerio; RNA Seq GSM8144968 r1 GSM8144968 1 1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP494974     DAPT_1_1.fq.gz DAPT_1_2.fq.gz fastq fastq 6917244000.0 34586220.0 GSM8144968 r1 0:100 1:100 A:1871550461;C:1566067610;G:1585361217;T:1894264712;N:0 100 100     1871550461 1566067610 1585361217 1894264712 0 SRX23938184 SRS20741665 SRA1823438 Institute of genetics, Zhejiang University Institute of genetics, Zhejiang University 2 0.9357 0.93705 0.09751 0.09758 0.67387 0.67363 0.51842 0.51997 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-03-13 Larval Larval Heart Cardiovascular System
30711 30711 SRR28329754 SRX23938183 SRS20741664 SRP494974 PRJNA1087264 Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression GSE261479 Transcriptome Analysis Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods: Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 µM were collected for RNA seq.   pubmed:40053597   DMSO 3 GSM8144967   source name:hearts|tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DMSO|geo loc name:missing|collection date:missing DMSO 3 Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix between treatment samples and wild type samples. hearts 60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 μM to 96 hpf. 1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer’s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h. tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DMSO GSM8144967 GSM8144967: DMSO 3; Danio rerio; RNA Seq GSM8144967 r1 GSM8144967 1 1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP494974     DMSO_3_2.fq.gz DMSO_3_1.fq.gz fastq fastq 6919708800.0 34598544.0 GSM8144967 r1 0:100 1:100 A:1894083722;C:1545002324;G:1569342322;T:1911280432;N:0 100 100     1894083722 1545002324 1569342322 1911280432 0 SRX23938183 SRS20741664 SRA1823438 Institute of genetics, Zhejiang University Institute of genetics, Zhejiang University 2 0.93873 0.93836 0.10256 0.10261 0.66068 0.6616 0.52724 0.52601 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-03-13 Larval Larval Heart Cardiovascular System
30712 30712 SRR28329755 SRX23938182 SRS20741663 SRP494974 PRJNA1087264 Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression GSE261479 Transcriptome Analysis Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods: Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 µM were collected for RNA seq.   pubmed:40053597   DMSO 2 GSM8144966   source name:hearts|tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DMSO|geo loc name:missing|collection date:missing DMSO 2 Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix between treatment samples and wild type samples. hearts 60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 μM to 96 hpf. 1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer’s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h. tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DMSO GSM8144966 GSM8144966: DMSO 2; Danio rerio; RNA Seq GSM8144966 r1 GSM8144966 1 1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP494974     DMSO_2_1.fq.gz DMSO_2_2.fq.gz fastq fastq 6902487800.0 34512439.0 GSM8144966 r1 0:100 1:100 A:1892099736;C:1540950565;G:1559704613;T:1909732886;N:0 100 100     1892099736 1540950565 1559704613 1909732886 0 SRX23938182 SRS20741663 SRA1823438 Institute of genetics, Zhejiang University Institute of genetics, Zhejiang University 2 0.93535 0.93511 0.10112 0.10162 0.66541 0.66592 0.51543 0.51644 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-03-13 Larval Larval Heart Cardiovascular System
30713 30713 SRR28329756 SRX23938181 SRS20741662 SRP494974 PRJNA1087264 Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression GSE261479 Transcriptome Analysis Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods: Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 µM were collected for RNA seq.   pubmed:40053597   DMSO 1 GSM8144965   source name:hearts|tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DMSO|geo loc name:missing|collection date:missing DMSO 1 Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix between treatment samples and wild type samples. hearts 60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 μM to 96 hpf. 1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer’s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h. tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DMSO GSM8144965 GSM8144965: DMSO 1; Danio rerio; RNA Seq GSM8144965 r1 GSM8144965 1 1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP494974     DMSO_1_1.fq.gz DMSO_1_2.fq.gz fastq fastq 6918299800.0 34591499.0 GSM8144965 r1 0:100 1:100 A:1887082093;C:1551476280;G:1575428027;T:1904313400;N:0 100 100     1887082093 1551476280 1575428027 1904313400 0 SRX23938181 SRS20741662 SRA1823438 Institute of genetics, Zhejiang University Institute of genetics, Zhejiang University 2 0.93809 0.93843 0.098 0.09793 0.66647 0.66709 0.53463 0.52582 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-03-13 Larval Larval Heart Cardiovascular System
31545 31545 SRR28435452 SRX24039370 SRS20832135 SRP497581 PRJNA1091566 The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration GSE262351 Transcriptome Analysis The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration but many questions remain about its exact role. Here we show that MyD88 a key component of the innate immune response controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration. We find in cryoinjured myd88 / ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population. Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 / endocardium and increased myofibroblasts and scarring. Notably endothelial specific overexpression of myd88 reverses these neutrophil fibrotic and scarring phenotypes. Mechanistically we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway and using loss and gain of function tools show that it controls neutrophil recruitment. Altogether these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: Aim: Investigation of the MyD88 signaling in endocardial cells during zebrafish cardiac regeneration. Methods: Endocardial cells sorted from the ETkrt4:EGFPsqet33 1A line at 96 hours post cryoinjury hpci. Conditions: 3 myd88+/+ and 3 myd88 / samples   pubmed:39271818   myd88 3 GSM8163706   tissue:endocardial|cell type:endocardial|genotype:myd88 / |time:96 hpci|geo loc name:missing|collection date:missing myd88 3 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 109 with STAR 2.7.10a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Assembly: danRer11 Supplementary files format and content: The tab delimited matrix shows DESeq normalized gene counts. endocardial   RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 / ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification. For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification. The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms according to effective library concentration and data amount.   cell type:endocardial|genotype:myd88 / |time:96 hpci GSM8163706 GSM8163706: myd88 3; Danio rerio; RNA Seq GSM8163706 r1 GSM8163706 1 RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 / ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification. For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification. The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms according to effective library concentration and data amount.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP497581   loader:fastq load.py myd88_3_1.fq.gz myd88_3_2.fq.gz fastq fastq 6626254800.0 22087516.0 GSM8163706 r1 0:150 1:150 A:1858405504;C:1462442884;G:1470757827;T:1834548220;N:100365 150 150     1858405504 1462442884 1470757827 1834548220 100365 SRX24039370 SRS20832135 SRA1832826 Bioinformatics, Max-Planck-Institute for Heart and Lung Research Bioinformatics, Max-Planck-Institute for Heart and Lung Research                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Germany 2024-03-25 Undetermined Undetermined Heart Cardiovascular System
31546 31546 SRR28435455 SRX24039369 SRS20832134 SRP497581 PRJNA1091566 The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration GSE262351 Transcriptome Analysis The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration but many questions remain about its exact role. Here we show that MyD88 a key component of the innate immune response controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration. We find in cryoinjured myd88 / ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population. Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 / endocardium and increased myofibroblasts and scarring. Notably endothelial specific overexpression of myd88 reverses these neutrophil fibrotic and scarring phenotypes. Mechanistically we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway and using loss and gain of function tools show that it controls neutrophil recruitment. Altogether these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: Aim: Investigation of the MyD88 signaling in endocardial cells during zebrafish cardiac regeneration. Methods: Endocardial cells sorted from the ETkrt4:EGFPsqet33 1A line at 96 hours post cryoinjury hpci. Conditions: 3 myd88+/+ and 3 myd88 / samples   pubmed:39271818   myd88 2 GSM8163705   tissue:endocardial|cell type:endocardial|genotype:myd88 / |time:96 hpci|geo loc name:missing|collection date:missing myd88 2 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 109 with STAR 2.7.10a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Assembly: danRer11 Supplementary files format and content: The tab delimited matrix shows DESeq normalized gene counts. endocardial   RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 / ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification. For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification. The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms according to effective library concentration and data amount.   cell type:endocardial|genotype:myd88 / |time:96 hpci GSM8163705 GSM8163705: myd88 2; Danio rerio; RNA Seq GSM8163705 r1 GSM8163705 1 RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 / ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification. For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification. The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms according to effective library concentration and data amount.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP497581   loader:fastq load.py myd88_2_1.fq.gz myd88_2_2.fq.gz fastq fastq 6586163100.0 21953877.0 GSM8163705 r1 0:150 1:150 A:1856129657;C:1440403994;G:1451543521;T:1837982507;N:103421 150 150     1856129657 1440403994 1451543521 1837982507 103421 SRX24039369 SRS20832134 SRA1832826 Bioinformatics, Max-Planck-Institute for Heart and Lung Research Bioinformatics, Max-Planck-Institute for Heart and Lung Research                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Germany 2024-03-25 Undetermined Undetermined Heart Cardiovascular System
31547 31547 SRR28435453 SRX24039368 SRS20832133 SRP497581 PRJNA1091566 The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration GSE262351 Transcriptome Analysis The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration but many questions remain about its exact role. Here we show that MyD88 a key component of the innate immune response controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration. We find in cryoinjured myd88 / ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population. Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 / endocardium and increased myofibroblasts and scarring. Notably endothelial specific overexpression of myd88 reverses these neutrophil fibrotic and scarring phenotypes. Mechanistically we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway and using loss and gain of function tools show that it controls neutrophil recruitment. Altogether these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: Aim: Investigation of the MyD88 signaling in endocardial cells during zebrafish cardiac regeneration. Methods: Endocardial cells sorted from the ETkrt4:EGFPsqet33 1A line at 96 hours post cryoinjury hpci. Conditions: 3 myd88+/+ and 3 myd88 / samples   pubmed:39271818   myd88 1 GSM8163704   tissue:endocardial|cell type:endocardial|genotype:myd88 / |time:96 hpci|geo loc name:missing|collection date:missing myd88 1 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 109 with STAR 2.7.10a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Assembly: danRer11 Supplementary files format and content: The tab delimited matrix shows DESeq normalized gene counts. endocardial   RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 / ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification. For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification. The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms according to effective library concentration and data amount.   cell type:endocardial|genotype:myd88 / |time:96 hpci GSM8163704 GSM8163704: myd88 1; Danio rerio; RNA Seq GSM8163704 r1 GSM8163704 1 RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 / ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification. For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification. The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms according to effective library concentration and data amount.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP497581   loader:fastq load.py myd88_1_1.fq.gz myd88_1_2.fq.gz fastq fastq 6586212900.0 21954043.0 GSM8163704 r1 0:150 1:150 A:1835825607;C:1467677697;G:1474870953;T:1807740616;N:98027 150 150     1835825607 1467677697 1474870953 1807740616 98027 SRX24039368 SRS20832133 SRA1832826 Bioinformatics, Max-Planck-Institute for Heart and Lung Research Bioinformatics, Max-Planck-Institute for Heart and Lung Research                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Germany 2024-03-25 Undetermined Undetermined Heart Cardiovascular System
31548 31548 SRR28435454 SRX24039367 SRS20832132 SRP497581 PRJNA1091566 The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration GSE262351 Transcriptome Analysis The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration but many questions remain about its exact role. Here we show that MyD88 a key component of the innate immune response controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration. We find in cryoinjured myd88 / ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population. Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 / endocardium and increased myofibroblasts and scarring. Notably endothelial specific overexpression of myd88 reverses these neutrophil fibrotic and scarring phenotypes. Mechanistically we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway and using loss and gain of function tools show that it controls neutrophil recruitment. Altogether these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: Aim: Investigation of the MyD88 signaling in endocardial cells during zebrafish cardiac regeneration. Methods: Endocardial cells sorted from the ETkrt4:EGFPsqet33 1A line at 96 hours post cryoinjury hpci. Conditions: 3 myd88+/+ and 3 myd88 / samples   pubmed:39271818   WT 3 GSM8163703   tissue:endocardial|cell type:endocardial|genotype:myd88+/+|time:96 hpci|geo loc name:missing|collection date:missing WT 3 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 109 with STAR 2.7.10a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Assembly: danRer11 Supplementary files format and content: The tab delimited matrix shows DESeq normalized gene counts. endocardial   RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 / ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification. For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification. The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms according to effective library concentration and data amount.   cell type:endocardial|genotype:myd88+/+|time:96 hpci GSM8163703 GSM8163703: WT 3; Danio rerio; RNA Seq GSM8163703 r1 GSM8163703 1 RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 / ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification. For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification. The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms according to effective library concentration and data amount.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP497581   loader:fastq load.py WT_3_1.fq.gz WT_3_2.fq.gz fastq fastq 6554345400.0 21847818.0 GSM8163703 r1 0:150 1:150 A:1829151207;C:1459298563;G:1466145928;T:1799650897;N:98805 150 150     1829151207 1459298563 1466145928 1799650897 98805 SRX24039367 SRS20832132 SRA1832826 Bioinformatics, Max-Planck-Institute for Heart and Lung Research Bioinformatics, Max-Planck-Institute for Heart and Lung Research                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Germany 2024-03-25 Undetermined Undetermined Heart Cardiovascular System
31549 31549 SRR28435456 SRX24039366 SRS20832131 SRP497581 PRJNA1091566 The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration GSE262351 Transcriptome Analysis The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration but many questions remain about its exact role. Here we show that MyD88 a key component of the innate immune response controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration. We find in cryoinjured myd88 / ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population. Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 / endocardium and increased myofibroblasts and scarring. Notably endothelial specific overexpression of myd88 reverses these neutrophil fibrotic and scarring phenotypes. Mechanistically we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway and using loss and gain of function tools show that it controls neutrophil recruitment. Altogether these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: Aim: Investigation of the MyD88 signaling in endocardial cells during zebrafish cardiac regeneration. Methods: Endocardial cells sorted from the ETkrt4:EGFPsqet33 1A line at 96 hours post cryoinjury hpci. Conditions: 3 myd88+/+ and 3 myd88 / samples   pubmed:39271818   WT 2 GSM8163702   tissue:endocardial|cell type:endocardial|genotype:myd88+/+|time:96 hpci|geo loc name:missing|collection date:missing WT 2 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 109 with STAR 2.7.10a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Assembly: danRer11 Supplementary files format and content: The tab delimited matrix shows DESeq normalized gene counts. endocardial   RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 / ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification. For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification. The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms according to effective library concentration and data amount.   cell type:endocardial|genotype:myd88+/+|time:96 hpci GSM8163702 GSM8163702: WT 2; Danio rerio; RNA Seq GSM8163702 r1 GSM8163702 1 RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 / ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification. For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification. The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms according to effective library concentration and data amount.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP497581   loader:fastq load.py WT_2_1.fq.gz WT_2_2.fq.gz fastq fastq 6440692500.0 21468975.0 GSM8163702 r1 0:150 1:150 A:1797022330;C:1433189990;G:1440263369;T:1770115464;N:101347 150 150     1797022330 1433189990 1440263369 1770115464 101347 SRX24039366 SRS20832131 SRA1832826 Bioinformatics, Max-Planck-Institute for Heart and Lung Research Bioinformatics, Max-Planck-Institute for Heart and Lung Research                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Germany 2024-03-25 Undetermined Undetermined Heart Cardiovascular System
31550 31550 SRR28435457 SRX24039365 SRS20832130 SRP497581 PRJNA1091566 The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration GSE262351 Transcriptome Analysis The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration but many questions remain about its exact role. Here we show that MyD88 a key component of the innate immune response controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration. We find in cryoinjured myd88 / ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population. Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 / endocardium and increased myofibroblasts and scarring. Notably endothelial specific overexpression of myd88 reverses these neutrophil fibrotic and scarring phenotypes. Mechanistically we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway and using loss and gain of function tools show that it controls neutrophil recruitment. Altogether these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: Aim: Investigation of the MyD88 signaling in endocardial cells during zebrafish cardiac regeneration. Methods: Endocardial cells sorted from the ETkrt4:EGFPsqet33 1A line at 96 hours post cryoinjury hpci. Conditions: 3 myd88+/+ and 3 myd88 / samples   pubmed:39271818   WT 1 GSM8163701   tissue:endocardial|cell type:endocardial|genotype:myd88+/+|time:96 hpci|geo loc name:missing|collection date:missing WT 1 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 109 with STAR 2.7.10a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Assembly: danRer11 Supplementary files format and content: The tab delimited matrix shows DESeq normalized gene counts. endocardial   RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 / ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification. For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification. The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms according to effective library concentration and data amount.   cell type:endocardial|genotype:myd88+/+|time:96 hpci GSM8163701 GSM8163701: WT 1; Danio rerio; RNA Seq GSM8163701 r1 GSM8163701 1 RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 / ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification. For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification. The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms according to effective library concentration and data amount.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP497581   loader:fastq load.py WT_1_1.fq.gz WT_1_2.fq.gz fastq fastq 6343747500.0 21145825.0 GSM8163701 r1 0:150 1:150 A:1783890425;C:1396753566;G:1403241010;T:1759774134;N:88365 150 150     1783890425 1396753566 1403241010 1759774134 88365 SRX24039365 SRS20832130 SRA1832826 Bioinformatics, Max-Planck-Institute for Heart and Lung Research Bioinformatics, Max-Planck-Institute for Heart and Lung Research                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Germany 2024-03-25 Undetermined Undetermined Heart Cardiovascular System
31715 31715 SRR28508805 SRX24109965 SRS20897113 SRP498846 PRJNA1094457 Danio rerio Transcriptome or Gene expression PRJNA1094457 Other Atrial cardiomyopathy which often comes with underlying genetic defects has been recognized as a possible substrate of atrial fibrillation. MYH6 encodes a myosin heavy chain a MHC predominantly expressed in the atria and pivotal in sarcomere organization and muscle contraction. However the role of MYH6 in atrial diseases has not been fully elucidated and the genetic cause of atrial cardiomyopathy needs further investigation. Here we employed CRISPR/Cas9 to generate myh6 knockout zebrafish assessing cardiac function through diverse methodologies including video analysis ECG echocardiography transmission electron microscopy and transcriptomic sequencing. Our findings revealed that myh6 defects in zebrafish led to impaired atrial and ventricular function and disordered sarcomere. This research underscores the pivotal role of MYH6 in maintaining atrial function and development. The observed connections between sarcomeric gene variants and atrial cardiomyopathy contribute to our understanding of the genetic basis of atrial fibrillation.       myh6+/ 3 Sample 6   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:6 mpf|dev stage:not collected|collection date:2023 09 03|geo loc name:not collected|sex:pooled male and female|tissue:heart|genotype:myh6+/ |BioSampleModel:Model organism or animal                 myh6+/ 3 Sample 6 Sample 6 Sequencing data were analyzed by R studio Version 2023.03.0+386. Differentially expressed genes DEGs between the experimental myh6+/ and control wildtype groups were identified using the DESeq2 package.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498846     7_230906N_S64_L004_R1_001.fastq.gz 7_230906N_S64_L004_R2_001.fastq.gz fastq fastq 5096818364.0 16876882.0 7 230906N S64 L004 R1 001.fastq.gz 0:151 1:151 A:1417476599;C:1123713516;G:1180970526;T:1374564888;N:92835 151 151     1417476599 1123713516 1180970526 1374564888 92835 SRX24109965 SRS20897113 SRA1836610 Nanjing medical university|Cardiology Nanjing medical university 2 0.92843 0.93025 0.09825 0.0937 0.7601 0.76081 0.46245 0.45548 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-31 Adult Adult Heart Cardiovascular System
31716 31716 SRR28508806 SRX24109964 SRS20897112 SRP498846 PRJNA1094457 Danio rerio Transcriptome or Gene expression PRJNA1094457 Other Atrial cardiomyopathy which often comes with underlying genetic defects has been recognized as a possible substrate of atrial fibrillation. MYH6 encodes a myosin heavy chain a MHC predominantly expressed in the atria and pivotal in sarcomere organization and muscle contraction. However the role of MYH6 in atrial diseases has not been fully elucidated and the genetic cause of atrial cardiomyopathy needs further investigation. Here we employed CRISPR/Cas9 to generate myh6 knockout zebrafish assessing cardiac function through diverse methodologies including video analysis ECG echocardiography transmission electron microscopy and transcriptomic sequencing. Our findings revealed that myh6 defects in zebrafish led to impaired atrial and ventricular function and disordered sarcomere. This research underscores the pivotal role of MYH6 in maintaining atrial function and development. The observed connections between sarcomeric gene variants and atrial cardiomyopathy contribute to our understanding of the genetic basis of atrial fibrillation.       myh6+/ 2 Sample 5   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:6 mpf|dev stage:not collected|collection date:2023 09 03|geo loc name:not collected|sex:pooled male and female|tissue:heart|genotype:myh6+/ |BioSampleModel:Model organism or animal                 myh6+/ 2 Sample 5 Sample 5 Sequencing data were analyzed by R studio Version 2023.03.0+386. Differentially expressed genes DEGs between the experimental myh6+/ and control wildtype groups were identified using the DESeq2 package.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498846     5_230906N_S62_L004_R2_001.fastq.gz 5_230906N_S62_L004_R1_001.fastq.gz fastq fastq 6194790402.0 20512551.0 5 230906N S62 L004 R1 001.fastq.gz 0:151 1:151 A:1714858851;C:1363381540;G:1448185824;T:1668247206;N:116981 151 151     1714858851 1363381540 1448185824 1668247206 116981 SRX24109964 SRS20897112 SRA1836610 Nanjing medical university|Cardiology Nanjing medical university 2 0.93019 0.93196 0.09367 0.08848 0.75444 0.75741 0.48694 0.48749 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-31 Adult Adult Heart Cardiovascular System

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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");;