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run_metadata

6,544 rows where experiment.library_selection = "cDNA", tissue_curation = "Embryo Imprecise" and tissue_curation_coarse = "All anatomical structures"

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technology >10

devstage_curation >10

experiment.platform 6

devstage_curation_coarse 5

experiment.library_strategy 3

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

  • All anatomical structures · 6,544 ✖

tissue_curation 1

  • Embryo Imprecise · 6,544 ✖

experiment.library_selection 1

  • cDNA · 6,544 ✖
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
3015 3015 ERR1396841 ERX1468100 ERS1051448 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 C7 SAMEA3864314 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864314|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:35Z|INSDC status:public|Submitter Id:2a85d100 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a85d100 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#24 15616955 Illumina sequencing of library 15616955 constructed from sample accession ERS1051448 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence ATTCCT. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#24.cram cram 252742350.0 5054847.0 SC RUN 18732 2#24 0:50 A:72444190;C:64568625;G:62796637;T:52911792;N:21106 50       72444190 64568625 62796637 52911792 21106 ERX1468100 ERS1051448 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.61824   0.09608   0.8842   0.56978   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Embryo Imprecise All anatomical structures
3039 3039 ERR1396817 ERX1468076 ERS1051448 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 C7 SAMEA3864314 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864314|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:35Z|INSDC status:public|Submitter Id:2a85d100 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a85d100 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#24 15616955 Illumina sequencing of library 15616955 constructed from sample accession ERS1051448 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ATTCCT. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#24.cram cram 258624300.0 5172486.0 SC RUN 18732 1#24 0:50 A:74123846;C:66047722;G:64286422;T:54141623;N:24687 50       74123846 66047722 64286422 54141623 24687 ERX1468076 ERS1051448 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.62009   0.09612   0.88434   0.55718   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Embryo Imprecise All anatomical structures
9419 9419 ERR273825 ERX248101 ERS092357 ERP001559 PRJEB3118 Zebrafish transcript profiling Zebrafish_transcript_profiling-sc-2012-06-28T15:47:32Z-82 Transcriptome Analysis Paired end sequence data from the Illumina Genome Analyzer was prepared from normal and mutant zebrafish embryos for transcript profiling. This includes pilot studies for transcript indexing within the sequence reads.         SAMEA1888984 SC ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 05 13T11:13:14Z|ENA LAST UPDATE:2018 03 08T15:36:21Z|External Id:SAMEA1888984|INSDC center name:SC|INSDC first public:2013 05 13T11:13:14Z|INSDC last update:2018 03 08T15:36:21Z|INSDC status:public|Submitter Id:hu2117 mutant vs wild type sc 2012 02 06T13:11:11Z 1107268|common name:zebrafish|sample description:3 prime end enriched mRNA from 3 morphological mutant hu2117 embryo samples and 3 matched sibling wild type samples. A 6 base indexing sequence is bases 5 to 10 of read 1 followed by polyT.|sample name:hu2117 mutant vs wild type sc 2012 02 06T13:11:11Z 1107268|scientific name:Danio rerio                 1 SC EXP 6316 8 2387558 Illumina sequencing of library 2387558 constructed from sample accession ERS092357 for study accession ERP001559. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP001559 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 05 13|ENA LAST UPDATE:2018 11 16 6316_8.bam bam 12715227300.0 84768182.0 SC RUN 6316 8 0:75 1:75 A:3986328155;C:1983554902;G:2466211000;T:4277430579;N:1702664 75 75     3986328155 1983554902 2466211000 4277430579 1702664 ERX248101 ERS092357 ERA212579 SC Wellcome Sanger Institute 2 0.06657 0.60346 0.04569 0.19203 0.9767 0.82014 0.52373 0.4048 75 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-05-13 Undetermined Embryo Embryo Imprecise All anatomical structures
9420 9420 ERR273824 ERX248100 ERS092356 ERP001559 PRJEB3118 Zebrafish transcript profiling Zebrafish_transcript_profiling-sc-2012-06-28T15:47:32Z-82 Transcriptome Analysis Paired end sequence data from the Illumina Genome Analyzer was prepared from normal and mutant zebrafish embryos for transcript profiling. This includes pilot studies for transcript indexing within the sequence reads.         SAMEA1889000 SC ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 05 13T11:13:13Z|ENA LAST UPDATE:2018 03 08T15:36:25Z|External Id:SAMEA1889000|INSDC center name:SC|INSDC first public:2013 05 13T11:13:13Z|INSDC last update:2018 03 08T15:36:25Z|INSDC status:public|Submitter Id:e48 mutant vs wild type sc 2012 02 06T13:11:09Z 1107267|common name:zebrafish|sample description:3 prime end enriched mRNA from 3 morphological mutant e48 embryo samples and 3 matched sibling wild type samples. A 6 base indexing sequence is bases 5 to 10 of read 1 followed by polyT.|sample name:e48 mutant vs wild type sc 2012 02 06T13:11:09Z 1107267|scientific name:Danio rerio                 1 SC EXP 6316 7 2387557 Illumina sequencing of library 2387557 constructed from sample accession ERS092356 for study accession ERP001559. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP001559 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 05 13|ENA LAST UPDATE:2018 11 16 6316_7.bam bam 17475932100.0 116506214.0 SC RUN 6316 7 0:75 1:75 A:5548228936;C:2693024343;G:3365940794;T:5867204994;N:1533033 75 75     5548228936 2693024343 3365940794 5867204994 1533033 ERX248100 ERS092356 ERA212579 SC Wellcome Sanger Institute 2 0.05939 0.59457 0.04089 0.19671 0.98068 0.838 0.46304 0.62741 75 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-05-13 Undetermined Embryo Embryo Imprecise All anatomical structures
9421 9421 ERR273823 ERX248099 ERS092354 ERP001559 PRJEB3118 Zebrafish transcript profiling Zebrafish_transcript_profiling-sc-2012-06-28T15:47:32Z-82 Transcriptome Analysis Paired end sequence data from the Illumina Genome Analyzer was prepared from normal and mutant zebrafish embryos for transcript profiling. This includes pilot studies for transcript indexing within the sequence reads.         SAMEA1889008 SC ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 05 13T11:13:13Z|ENA LAST UPDATE:2018 03 08T15:36:21Z|External Id:SAMEA1889008|INSDC center name:SC|INSDC first public:2013 05 13T11:13:13Z|INSDC last update:2018 03 08T15:36:21Z|INSDC status:public|Submitter Id:hu3332 mutant vs wild type sc 2012 02 06T13:11:07Z 1107265|common name:zebrafish|sample description:3 prime end enriched mRNA from 3 morphological mutant hu3332 embryo samples and 3 matched sibling wild type samples. A 6 base indexing sequence is bases 5 to 10 of read 1 followed by polyT.|sample name:hu3332 mutant vs wild type sc 2012 02 06T13:11:07Z 1107265|scientific name:Danio rerio                 1 SC EXP 6316 5 2387555 Illumina sequencing of library 2387555 constructed from sample accession ERS092354 for study accession ERP001559. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP001559 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 05 13|ENA LAST UPDATE:2018 11 16 6316_5.bam bam 13995917850.0 93306119.0 SC RUN 6316 5 0:75 1:75 A:4367273029;C:2176748810;G:2714026832;T:4736121060;N:1748119 75 75     4367273029 2176748810 2714026832 4736121060 1748119 ERX248099 ERS092354 ERA212579 SC Wellcome Sanger Institute 2 0.06401 0.62019 0.04224 0.18728 0.97723 0.81071 0.461 0.55379 75 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-05-13 Undetermined Embryo Embryo Imprecise All anatomical structures
9422 9422 ERR273822 ERX248098 ERS092063 ERP001559 PRJEB3118 Zebrafish transcript profiling Zebrafish_transcript_profiling-sc-2012-06-28T15:47:32Z-82 Transcriptome Analysis Paired end sequence data from the Illumina Genome Analyzer was prepared from normal and mutant zebrafish embryos for transcript profiling. This includes pilot studies for transcript indexing within the sequence reads.         SAMEA1888996 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 05 13T11:13:13Z|ENA LAST UPDATE:2018 03 08T15:36:13Z|External Id:SAMEA1888996|INSDC center name:SC|INSDC first public:2013 05 13T11:13:13Z|INSDC last update:2018 03 08T15:36:13Z|INSDC status:public|Submitter Id:sa0058 mutant vs wild type sc 2012 02 06T13:05:07Z 265521|common name:zebrafish|sample description:33 prime end enriched mRNA from 3 morphological mutant sa0058 embryo samples and 3 matched sibling wild type samples. A 6 base indexing sequence is bases 5 to 10 of read 1 followed by polyT.|sample name:sa0058 mutant vs wild type sc 2012 02 06T13:05:07Z 265521|scientific name:Danio rerio                 1 SC EXP 5287 7 449230 Illumina sequencing of library 449230 constructed from sample accession ERS092063 for study accession ERP001559. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer II   ERP001559 Illumina Genome Analyzer II paired end sequencing ENA FIRST PUBLIC:2013 05 13|ENA LAST UPDATE:2018 11 16 5287_7.bam bam 2216402460.0 20522245.0 SC RUN 5287 7 0:54 1:54 A:646882787;C:346392353;G:394060191;T:827745173;N:1321956 54 54     646882787 346392353 394060191 827745173 1321956 ERX248098 ERS092063 ERA212579 SC Wellcome Sanger Institute 2 0.02565 0.72009 0.01691 0.21429 0.98725 0.78944 0.62084 0.61278 54 54 T B mate1 technical by mapping diff illumina early_illumina 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-05-13 Undetermined Embryo Embryo Imprecise All anatomical structures
11245 11245 ERR10851251 ERX10296231 ERS14601258 ERP144652 PRJEB59599 Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E-MTAB-12577 Transcriptome Analysis Comparison between wildtype and Gata2b heterozygous zebrafish HSPCs ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17   Protocols: Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified WT3 cd41pflt1p48hpf SAMEA112483908 Department of Hematology cancer institute ErasmusMC ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17|External Id:SAMEA112483908|INSDC center alias:Department of Hematology cancer institute ErasmusMC|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC first public:2023 02 17T00:21:53Z|INSDC last update:2023 02 17T00:21:53Z|INSDC status:public|Submitter Id:E MTAB 12577:WT3 cd41pflt1p48hpf|age:48|broker name:ArrayExpress|cell type:hematopoietic stem cell|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|immunophenotype:CD41:GFP+ Flt1:RFP+|individual:pools of 3 embryos 1|organism part:liver|sample name:E MTAB 12577:WT3 cd41pflt1p48hpf|scientific name:Danio rerio|strain:TgCD41:GFP TgFlt1:RFP WT                 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E MTAB 12577:WT3 cd41pflt1p48hpf p WT3 cd41pflt1p48hpf p Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP144652 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17 WT3_cd41pflt1p48hpf_R1.fastq.gz WT3_cd41pflt1p48hpf_R2.fastq.gz fastq fastq 2865896816.0 14187608.0 E MTAB 12577:WT3 cd41pflt1p48hpf R 0:101 1:101 A:766433553;C:631932872;G:660672891;T:806849737;N:7763 101 101     766433553 631932872 660672891 806849737 7763 ERX10296231 ERS14601258 ERA20429817 Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive 2 0.90501 0.85042 0.09405 0.09335 0.87286 0.87943 0.48423 0.47904 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Netherlands 2023-02-17 Hatching Embryo Embryo Imprecise All anatomical structures
11246 11246 ERR10851250 ERX10296230 ERS14601257 ERP144652 PRJEB59599 Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E-MTAB-12577 Transcriptome Analysis Comparison between wildtype and Gata2b heterozygous zebrafish HSPCs ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17   Protocols: Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified WT2 cd41pflt1p48hpf SAMEA112483907 Department of Hematology cancer institute ErasmusMC ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17|External Id:SAMEA112483907|INSDC center alias:Department of Hematology cancer institute ErasmusMC|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC first public:2023 02 17T00:21:53Z|INSDC last update:2023 02 17T00:21:53Z|INSDC status:public|Submitter Id:E MTAB 12577:WT2 cd41pflt1p48hpf|age:48|broker name:ArrayExpress|cell type:hematopoietic stem cell|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|immunophenotype:CD41:GFP+ Flt1:RFP+|individual:pools of 3 embryos 5|organism part:liver|sample name:E MTAB 12577:WT2 cd41pflt1p48hpf|scientific name:Danio rerio|strain:TgCD41:GFP TgFlt1:RFP WT                 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E MTAB 12577:WT2 cd41pflt1p48hpf p WT2 cd41pflt1p48hpf p Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP144652 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17 WT2_cd41pflt1p48hpf_R1.fastq.gz WT2_cd41pflt1p48hpf_R2.fastq.gz fastq fastq 2929743360.0 14503680.0 E MTAB 12577:WT2 cd41pflt1p48hpf R 0:101 1:101 A:803775344;C:639485652;G:661899077;T:824575679;N:7608 101 101     803775344 639485652 661899077 824575679 7608 ERX10296230 ERS14601257 ERA20429817 Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive 2 0.94558 0.90768 0.09379 0.09399 0.79058 0.79833 0.48216 0.47743 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Netherlands 2023-02-17 Hatching Embryo Embryo Imprecise All anatomical structures
11247 11247 ERR10851249 ERX10296229 ERS14601256 ERP144652 PRJEB59599 Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E-MTAB-12577 Transcriptome Analysis Comparison between wildtype and Gata2b heterozygous zebrafish HSPCs ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17   Protocols: Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified WT1 cd41pflt1p48hpf SAMEA112483906 Department of Hematology cancer institute ErasmusMC ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17|External Id:SAMEA112483906|INSDC center alias:Department of Hematology cancer institute ErasmusMC|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC first public:2023 02 17T00:21:53Z|INSDC last update:2023 02 17T00:21:53Z|INSDC status:public|Submitter Id:E MTAB 12577:WT1 cd41pflt1p48hpf|age:48|broker name:ArrayExpress|cell type:hematopoietic stem cell|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|immunophenotype:CD41:GFP+ Flt1:RFP+|individual:pools of 3 embryos 4|organism part:liver|sample name:E MTAB 12577:WT1 cd41pflt1p48hpf|scientific name:Danio rerio|strain:TgCD41:GFP TgFlt1:RFP WT                 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E MTAB 12577:WT1 cd41pflt1p48hpf p WT1 cd41pflt1p48hpf p Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP144652 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17 WT1_cd41pflt1p48hpf_R1.fastq.gz WT1_cd41pflt1p48hpf_R2.fastq.gz fastq fastq 3248647426.0 16082413.0 E MTAB 12577:WT1 cd41pflt1p48hpf R 0:101 1:101 A:883030193;C:725566673;G:750551574;T:889489774;N:9212 101 101     883030193 725566673 750551574 889489774 9212 ERX10296229 ERS14601256 ERA20429817 Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive 2 0.91568 0.8915 0.09819 0.09602 0.86634 0.8706 0.48887 0.48731 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Netherlands 2023-02-17 Hatching Embryo Embryo Imprecise All anatomical structures
11248 11248 ERR10851248 ERX10296228 ERS14601255 ERP144652 PRJEB59599 Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E-MTAB-12577 Transcriptome Analysis Comparison between wildtype and Gata2b heterozygous zebrafish HSPCs ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17   Protocols: Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified Het3 cd41pflt1p48hpf SAMEA112483905 Department of Hematology cancer institute ErasmusMC ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17|External Id:SAMEA112483905|INSDC center alias:Department of Hematology cancer institute ErasmusMC|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC first public:2023 02 17T00:21:53Z|INSDC last update:2023 02 17T00:21:53Z|INSDC status:public|Submitter Id:E MTAB 12577:Het3 cd41pflt1p48hpf|age:48|broker name:ArrayExpress|cell type:hematopoietic stem cell|common name:zebrafish|developmental stage:embryo|genotype:Gata2b +/ |immunophenotype:CD41:GFP+ Flt1:RFP+|individual:pools of 3 embryos 3|organism part:liver|sample name:E MTAB 12577:Het3 cd41pflt1p48hpf|scientific name:Danio rerio|strain:TgCD41:GFP TgFlt1:RFP Gata2b KO                 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E MTAB 12577:Het3 cd41pflt1p48hpf p Het3 cd41pflt1p48hpf p Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified Experimental Factor: genotype:Gata2b +/ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP144652 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17 Het3_cd41pflt1p48hpf_R1.fastq.gz Het3_cd41pflt1p48hpf_R2.fastq.gz fastq fastq 2826011512.0 13990156.0 E MTAB 12577:Het3 cd41pflt1p48hpf R 0:101 1:101 A:777245323;C:622387331;G:640520737;T:785850577;N:7544 101 101     777245323 622387331 640520737 785850577 7544 ERX10296228 ERS14601255 ERA20429817 Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive 2 0.92716 0.90121 0.10896 0.10895 0.76739 0.77628 0.47007 0.46569 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Netherlands 2023-02-17 Hatching Embryo Embryo Imprecise All anatomical structures
11249 11249 ERR10851247 ERX10296227 ERS14601254 ERP144652 PRJEB59599 Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E-MTAB-12577 Transcriptome Analysis Comparison between wildtype and Gata2b heterozygous zebrafish HSPCs ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17   Protocols: Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified Het2 cd41pflt1p48hpf SAMEA112483904 Department of Hematology cancer institute ErasmusMC ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17|External Id:SAMEA112483904|INSDC center alias:Department of Hematology cancer institute ErasmusMC|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC first public:2023 02 17T00:21:53Z|INSDC last update:2023 02 17T00:21:53Z|INSDC status:public|Submitter Id:E MTAB 12577:Het2 cd41pflt1p48hpf|age:48|broker name:ArrayExpress|cell type:hematopoietic stem cell|common name:zebrafish|developmental stage:embryo|genotype:Gata2b +/ |immunophenotype:CD41:GFP+ Flt1:RFP+|individual:pools of 3 embryos 2|organism part:liver|sample name:E MTAB 12577:Het2 cd41pflt1p48hpf|scientific name:Danio rerio|strain:TgCD41:GFP TgFlt1:RFP Gata2b KO                 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E MTAB 12577:Het2 cd41pflt1p48hpf p Het2 cd41pflt1p48hpf p Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified Experimental Factor: genotype:Gata2b +/ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP144652 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17 Het2_cd41pflt1p48hpf_R1.fastq.gz Het2_cd41pflt1p48hpf_R2.fastq.gz fastq fastq 2999149954.0 14847277.0 E MTAB 12577:Het2 cd41pflt1p48hpf R 0:101 1:101 A:822247269;C:656610849;G:681974696;T:838308917;N:8223 101 101     822247269 656610849 681974696 838308917 8223 ERX10296227 ERS14601254 ERA20429817 Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive 2 0.94678 0.91473 0.10277 0.10053 0.76686 0.77684 0.46042 0.47202 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Netherlands 2023-02-17 Hatching Embryo Embryo Imprecise All anatomical structures
11250 11250 ERR10851246 ERX10296226 ERS14601253 ERP144652 PRJEB59599 Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E-MTAB-12577 Transcriptome Analysis Comparison between wildtype and Gata2b heterozygous zebrafish HSPCs ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17   Protocols: Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified Het1 cd41pflt1p48hpf SAMEA112483903 Department of Hematology cancer institute ErasmusMC ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17|External Id:SAMEA112483903|INSDC center alias:Department of Hematology cancer institute ErasmusMC|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC first public:2023 02 17T00:21:53Z|INSDC last update:2023 02 17T00:21:53Z|INSDC status:public|Submitter Id:E MTAB 12577:Het1 cd41pflt1p48hpf|age:48|broker name:ArrayExpress|cell type:hematopoietic stem cell|common name:zebrafish|developmental stage:embryo|genotype:Gata2b +/ |immunophenotype:CD41:GFP+ Flt1:RFP+|individual:pools of 3 embryos 1|organism part:liver|sample name:E MTAB 12577:Het1 cd41pflt1p48hpf|scientific name:Danio rerio|strain:TgCD41:GFP TgFlt1:RFP Gata2b KO                 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E MTAB 12577:Het1 cd41pflt1p48hpf p Het1 cd41pflt1p48hpf p Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified Experimental Factor: genotype:Gata2b +/ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP144652 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17 Het1_cd41pflt1p48hpf_R1.fastq.gz Het1_cd41pflt1p48hpf_R2.fastq.gz fastq fastq 36682350994.0 181595797.0 E MTAB 12577:Het1 cd41pflt1p48hpf R 0:101 1:101 A:10130106739;C:7969045717;G:8373740062;T:10209360741;N:97735 101 101     10130106739 7969045717 8373740062 10209360741 97735 ERX10296226 ERS14601253 ERA20429817 Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive 2 0.94302 0.91104 0.11873 0.11597 0.7554 0.76579 0.48813 0.47764 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Netherlands 2023-02-17 Hatching Embryo Embryo Imprecise All anatomical structures
15070 15070 ERR12476466 ERX11852287 ERS17743541 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1219 from a cross with a starved father 1219 Starved 1219S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:193 277029 1219S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1219S_S12_L003_R1_001.fastq.gz fastq 97592891.0 1298822.0 ena RUN TAB 15 01 2024 21:42:36:193 277030 0:75.14 A:34708924;C:19086989;G:21325291;T:22442527;N:29160 75       34708924 19086989 21325291 22442527 29160 ERX11852287 ERS17743541 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15071 15071 ERR12476447 ERX11852268 ERS17743536 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1203 from a cross with a fed father 1203 Fed 1203F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:179 276991 1203F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1203F_S5_L004_R1_001.fastq.gz fastq 92134036.0 1226106.0 ena RUN TAB 15 01 2024 21:42:36:179 276992 0:75.14 A:33032252;C:17497320;G:19713134;T:21873197;N:18133 75       33032252 17497320 19713134 21873197 18133 ERX11852268 ERS17743536 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15072 15072 ERR12476437 ERX11852258 ERS17743534 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1118 from a cross with a fed father 1118 Fed 1118F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:172 276971 1118F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1118F_S9_L002_R1_001.fastq.gz fastq 98606332.0 1311676.0 ena RUN TAB 15 01 2024 21:42:36:172 276972 0:75.18 A:35097475;C:19013865;G:21072825;T:23400976;N:21191 75       35097475 19013865 21072825 23400976 21191 ERX11852258 ERS17743534 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15073 15073 ERR12476468 ERX11852289 ERS17743542 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a fed father 1242D Fed 1242FD   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:194 277033 1242FD 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242FD_S13_L001_R1_001.fastq.gz fastq 89342488.0 1186885.0 ena RUN TAB 15 01 2024 21:42:36:194 277034 0:75.27 A:31174342;C:17129181;G:18704493;T:22323017;N:11455 75       31174342 17129181 18704493 22323017 11455 ERX11852289 ERS17743542 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15074 15074 ERR12476438 ERX11852259 ERS17743534 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1118 from a cross with a fed father 1118 Fed 1118F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:173 276973 1118F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1118F_S9_L003_R1_001.fastq.gz fastq 98443412.0 1309747.0 ena RUN TAB 15 01 2024 21:42:36:173 276974 0:75.16 A:35171021;C:18991511;G:20974950;T:23280285;N:25645 75       35171021 18991511 20974950 23280285 25645 ERX11852259 ERS17743534 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15075 15075 ERR12476442 ERX11852263 ERS17743535 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1118 from a cross with a starved father 1118 Starved 1118S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:176 276981 1118S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1118S_S10_L003_R1_001.fastq.gz fastq 98865255.0 1315357.0 ena RUN TAB 15 01 2024 21:42:36:176 276982 0:75.16 A:34981471;C:19126822;G:21304286;T:23427226;N:25450 75       34981471 19126822 21304286 23427226 25450 ERX11852263 ERS17743535 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15076 15076 ERR12476467 ERX11852288 ERS17743541 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1219 from a cross with a starved father 1219 Starved 1219S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:193 277031 1219S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1219S_S12_L004_R1_001.fastq.gz fastq 88230016.0 1174256.0 ena RUN TAB 15 01 2024 21:42:36:194 277032 0:75.14 A:31409300;C:17203675;G:19284478;T:20309174;N:23389 75       31409300 17203675 19284478 20309174 23389 ERX11852288 ERS17743541 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15077 15077 ERR12476470 ERX11852291 ERS17743542 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a fed father 1242D Fed 1242FD   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:195 277037 1242FD 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242FD_S13_L003_R1_001.fastq.gz fastq 93375090.0 1240903.0 ena RUN TAB 15 01 2024 21:42:36:196 277038 0:75.25 A:32510114;C:17950920;G:19575617;T:23324862;N:13577 75       32510114 17950920 19575617 23324862 13577 ERX11852291 ERS17743542 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15078 15078 ERR12476436 ERX11852257 ERS17743534 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1118 from a cross with a fed father 1118 Fed 1118F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:171 276969 1118F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1118F_S9_L001_R1_001.fastq.gz fastq 94258948.0 1253428.0 ena RUN TAB 15 01 2024 21:42:36:171 276970 0:75.20 A:33713614;C:18157124;G:20086205;T:22277451;N:24554 75       33713614 18157124 20086205 22277451 24554 ERX11852257 ERS17743534 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15079 15079 ERR12476452 ERX11852273 ERS17743538 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1210 from a cross with a fed father 1210 Fed 1210F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:183 277001 1210F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1210F_S7_L001_R1_001.fastq.gz fastq 96414625.0 1283672.0 ena RUN TAB 15 01 2024 21:42:36:183 277002 0:75.11 A:35605799;C:18366729;G:20807908;T:21594044;N:40145 75       35605799 18366729 20807908 21594044 40145 ERX11852273 ERS17743538 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15080 15080 ERR12476475 ERX11852296 ERS17743544 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a fed father 1242E Fed 1242FE   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:199 277047 1242FE 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242FE_S15_L004_R1_001.fastq.gz fastq 99581325.0 1325945.0 ena RUN TAB 15 01 2024 21:42:36:199 277048 0:75.10 A:36802442;C:18868511;G:20958294;T:22926783;N:25295 75       36802442 18868511 20958294 22926783 25295 ERX11852296 ERS17743544 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15082 15082 ERR12476473 ERX11852294 ERS17743544 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a fed father 1242E Fed 1242FE   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:198 277043 1242FE 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242FE_S15_L002_R1_001.fastq.gz fastq 111191327.0 1479982.0 ena RUN TAB 15 01 2024 21:42:36:198 277044 0:75.13 A:40873794;C:21118758;G:23508088;T:25663516;N:27171 75       40873794 21118758 23508088 25663516 27171 ERX11852294 ERS17743544 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15083 15083 ERR12476472 ERX11852293 ERS17743544 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a fed father 1242E Fed 1242FE   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:197 277041 1242FE 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242FE_S15_L001_R1_001.fastq.gz fastq 105936834.0 1409443.0 ena RUN TAB 15 01 2024 21:42:36:197 277042 0:75.16 A:39084749;C:20103850;G:22336806;T:24384711;N:26718 75       39084749 20103850 22336806 24384711 26718 ERX11852293 ERS17743544 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15084 15084 ERR12476455 ERX11852276 ERS17743538 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1210 from a cross with a fed father 1210 Fed 1210F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:185 277007 1210F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1210F_S7_L004_R1_001.fastq.gz fastq 91003627.0 1212716.0 ena RUN TAB 15 01 2024 21:42:36:185 277008 0:75.04 A:33677348;C:17299066;G:19585548;T:20403064;N:38601 75       33677348 17299066 19585548 20403064 38601 ERX11852276 ERS17743538 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15085 15085 ERR12476450 ERX11852271 ERS17743537 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1203 from a cross with a starved father 1203 Starved 1203S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:181 276997 1203S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1203S_S6_L003_R1_001.fastq.gz fastq 93998632.0 1251284.0 ena RUN TAB 15 01 2024 21:42:36:182 276998 0:75.12 A:33959433;C:18143368;G:20041026;T:21824242;N:30563 75       33959433 18143368 20041026 21824242 30563 ERX11852271 ERS17743537 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15086 15086 ERR12476446 ERX11852267 ERS17743536 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1203 from a cross with a fed father 1203 Fed 1203F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:178 276989 1203F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1203F_S5_L003_R1_001.fastq.gz fastq 102209965.0 1360067.0 ena RUN TAB 15 01 2024 21:42:36:179 276990 0:75.15 A:36554629;C:19466103;G:21890238;T:24276196;N:22799 75       36554629 19466103 21890238 24276196 22799 ERX11852267 ERS17743536 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15087 15087 ERR12476458 ERX11852279 ERS17743539 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1210 from a cross with a starved father 1210 Starved 1210S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:187 277013 1210S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1210S_S8_L003_R1_001.fastq.gz fastq 109602092.0 1466517.0 ena RUN TAB 15 01 2024 21:42:36:187 277014 0:74.74 A:42677564;C:20838229;G:24413347;T:21498031;N:174921 74       42677564 20838229 24413347 21498031 174921 ERX11852279 ERS17743539 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15088 15088 ERR12476453 ERX11852274 ERS17743538 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1210 from a cross with a fed father 1210 Fed 1210F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:183 277003 1210F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1210F_S7_L002_R1_001.fastq.gz fastq 100538748.0 1339248.0 ena RUN TAB 15 01 2024 21:42:36:184 277004 0:75.07 A:36966184;C:19156780;G:21758079;T:22618911;N:38794 75       36966184 19156780 21758079 22618911 38794 ERX11852274 ERS17743538 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15089 15089 ERR12476460 ERX11852281 ERS17743540 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1219 from a cross with a fed father 1219 Fed 1219F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:188 277017 1219F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1219F_S11_L001_R1_001.fastq.gz fastq 102219114.0 1358650.0 ena RUN TAB 15 01 2024 21:42:36:189 277018 0:75.24 A:35886099;C:19931420;G:22057068;T:24325918;N:18609 75       35886099 19931420 22057068 24325918 18609 ERX11852281 ERS17743540 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15090 15090 ERR12476451 ERX11852272 ERS17743537 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1203 from a cross with a starved father 1203 Starved 1203S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:182 276999 1203S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1203S_S6_L004_R1_001.fastq.gz fastq 84880221.0 1129985.0 ena RUN TAB 15 01 2024 21:42:36:182 277000 0:75.12 A:30708531;C:16338743;G:18094345;T:19712906;N:25696 75       30708531 16338743 18094345 19712906 25696 ERX11852272 ERS17743537 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15091 15091 ERR12476441 ERX11852262 ERS17743535 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1118 from a cross with a starved father 1118 Starved 1118S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:175 276979 1118S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1118S_S10_L002_R1_001.fastq.gz fastq 99340604.0 1321436.0 ena RUN TAB 15 01 2024 21:42:36:175 276980 0:75.18 A:34996267;C:19218610;G:21486623;T:23616635;N:22469 75       34996267 19218610 21486623 23616635 22469 ERX11852262 ERS17743535 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15092 15092 ERR12476440 ERX11852261 ERS17743535 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1118 from a cross with a starved father 1118 Starved 1118S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:174 276977 1118S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1118S_S10_L001_R1_001.fastq.gz fastq 94655454.0 1258724.0 ena RUN TAB 15 01 2024 21:42:36:175 276978 0:75.20 A:33514914;C:18282513;G:20410100;T:22427564;N:20363 75       33514914 18282513 20410100 22427564 20363 ERX11852261 ERS17743535 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15093 15093 ERR12476469 ERX11852290 ERS17743542 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a fed father 1242D Fed 1242FD   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:195 277035 1242FD 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242FD_S13_L002_R1_001.fastq.gz fastq 93346527.0 1240308.0 ena RUN TAB 15 01 2024 21:42:36:195 277036 0:75.26 A:32401771;C:17929540;G:19597511;T:23408465;N:9240 75       32401771 17929540 19597511 23408465 9240 ERX11852290 ERS17743542 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15094 15094 ERR12476462 ERX11852283 ERS17743540 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1219 from a cross with a fed father 1219 Fed 1219F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:190 277021 1219F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1219F_S11_L003_R1_001.fastq.gz fastq 106745726.0 1419461.0 ena RUN TAB 15 01 2024 21:42:36:190 277022 0:75.20 A:37396946;C:20851140;G:23075114;T:25400364;N:22162 75       37396946 20851140 23075114 25400364 22162 ERX11852283 ERS17743540 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15095 15095 ERR12476479 ERX11852300 ERS17743543 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a starved father 1242D Starved 1242SD   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:202 277055 1242SD 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242SD_S14_L004_R1_001.fastq.gz fastq 85586412.0 1137781.0 ena RUN TAB 15 01 2024 21:42:36:202 277056 0:75.22 A:29963542;C:16621745;G:18219345;T:20761941;N:19839 75       29963542 16621745 18219345 20761941 19839 ERX11852300 ERS17743543 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15096 15096 ERR12476444 ERX11852265 ERS17743536 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1203 from a cross with a fed father 1203 Fed 1203F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:177 276985 1203F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1203F_S5_L001_R1_001.fastq.gz fastq 97624173.0 1298240.0 ena RUN TAB 15 01 2024 21:42:36:177 276986 0:75.20 A:34935070;C:18569640;G:20912883;T:23188491;N:18089 75       34935070 18569640 20912883 23188491 18089 ERX11852265 ERS17743536 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15097 15097 ERR12476471 ERX11852292 ERS17743542 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a fed father 1242D Fed 1242FD   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:196 277039 1242FD 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242FD_S13_L004_R1_001.fastq.gz fastq 83383881.0 1108207.0 ena RUN TAB 15 01 2024 21:42:36:196 277040 0:75.24 A:29091135;C:15949002;G:17455499;T:20878004;N:10241 75       29091135 15949002 17455499 20878004 10241 ERX11852292 ERS17743542 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15098 15098 ERR12476439 ERX11852260 ERS17743534 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1118 from a cross with a fed father 1118 Fed 1118F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:174 276975 1118F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1118F_S9_L004_R1_001.fastq.gz fastq 88439160.0 1176751.0 ena RUN TAB 15 01 2024 21:42:36:174 276976 0:75.16 A:31652556;C:16996499;G:18832233;T:20937970;N:19902 75       31652556 16996499 18832233 20937970 19902 ERX11852260 ERS17743534 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15099 15099 ERR12476449 ERX11852270 ERS17743537 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1203 from a cross with a starved father 1203 Starved 1203S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:181 276995 1203S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1203S_S6_L002_R1_001.fastq.gz fastq 94525103.0 1257985.0 ena RUN TAB 15 01 2024 21:42:36:181 276996 0:75.14 A:34035341;C:18242921;G:20233155;T:21988512;N:25174 75       34035341 18242921 20233155 21988512 25174 ERX11852270 ERS17743537 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15100 15100 ERR12476465 ERX11852286 ERS17743541 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1219 from a cross with a starved father 1219 Starved 1219S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:192 277027 1219S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1219S_S12_L002_R1_001.fastq.gz fastq 97087536.0 1291846.0 ena RUN TAB 15 01 2024 21:42:36:192 277028 0:75.15 A:34386434;C:18969192;G:21277103;T:22430566;N:24241 75       34386434 18969192 21277103 22430566 24241 ERX11852286 ERS17743541 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15101 15101 ERR12476482 ERX11852303 ERS17743545 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a starved father 1242E Starved 1242SE   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:204 277061 1242SE 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242SE_S16_L003_R1_001.fastq.gz fastq 119572581.0 1595036.0 ena RUN TAB 15 01 2024 21:42:36:204 277062 0:74.97 A:45069577;C:22967641;G:25483351;T:25959672;N:92340 74       45069577 22967641 25483351 25959672 92340 ERX11852303 ERS17743545 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15102 15102 ERR12476459 ERX11852280 ERS17743539 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1210 from a cross with a starved father 1210 Starved 1210S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:188 277015 1210S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1210S_S8_L004_R1_001.fastq.gz fastq 100688924.0 1347280.0 ena RUN TAB 15 01 2024 21:42:36:188 277016 0:74.73 A:39242841;C:19105480;G:22424580;T:19763164;N:152859 74       39242841 19105480 22424580 19763164 152859 ERX11852280 ERS17743539 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15103 15103 ERR12476481 ERX11852302 ERS17743545 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a starved father 1242E Starved 1242SE   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:203 277059 1242SE 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242SE_S16_L002_R1_001.fastq.gz fastq 119860507.0 1598259.0 ena RUN TAB 15 01 2024 21:42:36:204 277060 0:74.99 A:44981934;C:23018661;G:25670723;T:26114916;N:74273 74       44981934 23018661 25670723 26114916 74273 ERX11852302 ERS17743545 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15104 15104 ERR12476483 ERX11852304 ERS17743545 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a starved father 1242E Starved 1242SE   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:205 277063 1242SE 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242SE_S16_L004_R1_001.fastq.gz fastq 108782281.0 1451206.0 ena RUN TAB 15 01 2024 21:42:36:205 277064 0:74.96 A:41041986;C:20859560;G:23168159;T:23635345;N:77231 74       41041986 20859560 23168159 23635345 77231 ERX11852304 ERS17743545 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15105 15105 ERR12476448 ERX11852269 ERS17743537 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1203 from a cross with a starved father 1203 Starved 1203S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:180 276993 1203S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1203S_S6_L001_R1_001.fastq.gz fastq 89917861.0 1196172.0 ena RUN TAB 15 01 2024 21:42:36:180 276994 0:75.17 A:32511634;C:17340472;G:19179480;T:20857531;N:28744 75       32511634 17340472 19179480 20857531 28744 ERX11852269 ERS17743537 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15106 15106 ERR12476457 ERX11852278 ERS17743539 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1210 from a cross with a starved father 1210 Starved 1210S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:186 277011 1210S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1210S_S8_L002_R1_001.fastq.gz fastq 110304194.0 1474848.0 ena RUN TAB 15 01 2024 21:42:36:187 277012 0:74.79 A:42702966;C:20952577;G:24773042;T:21724801;N:150808 74       42702966 20952577 24773042 21724801 150808 ERX11852278 ERS17743539 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15107 15107 ERR12476456 ERX11852277 ERS17743539 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1210 from a cross with a starved father 1210 Starved 1210S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:185 277009 1210S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1210S_S8_L001_R1_001.fastq.gz fastq 106074722.0 1417003.0 ena RUN TAB 15 01 2024 21:42:36:186 277010 0:74.86 A:41208838;C:20151614;G:23770531;T:20792595;N:151144 74       41208838 20151614 23770531 20792595 151144 ERX11852277 ERS17743539 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15108 15108 ERR12476461 ERX11852282 ERS17743540 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1219 from a cross with a fed father 1219 Fed 1219F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:189 277019 1219F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1219F_S11_L002_R1_001.fastq.gz fastq 106799888.0 1420026.0 ena RUN TAB 15 01 2024 21:42:36:189 277020 0:75.21 A:37294667;C:20842952;G:23154298;T:25488653;N:19318 75       37294667 20842952 23154298 25488653 19318 ERX11852282 ERS17743540 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15109 15109 ERR12476480 ERX11852301 ERS17743545 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a starved father 1242E Starved 1242SE   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:203 277057 1242SE 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242SE_S16_L001_R1_001.fastq.gz fastq 115150299.0 1534621.0 ena RUN TAB 15 01 2024 21:42:36:203 277058 0:75.04 A:43393516;C:22116575;G:24607338;T:24954423;N:78447 75       43393516 22116575 24607338 24954423 78447 ERX11852301 ERS17743545 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15110 15110 ERR12476464 ERX11852285 ERS17743541 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1219 from a cross with a starved father 1219 Starved 1219S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:191 277025 1219S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1219S_S12_L001_R1_001.fastq.gz fastq 93625807.0 1245248.0 ena RUN TAB 15 01 2024 21:42:36:192 277026 0:75.19 A:33311180;C:18278250;G:20453262;T:21557661;N:25454 75       33311180 18278250 20453262 21557661 25454 ERX11852285 ERS17743541 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15111 15111 ERR12476474 ERX11852295 ERS17743544 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a fed father 1242E Fed 1242FE   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:198 277045 1242FE 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242FE_S15_L003_R1_001.fastq.gz fastq 110591461.0 1472278.0 ena RUN TAB 15 01 2024 21:42:36:199 277046 0:75.12 A:40767831;C:21026089;G:23298123;T:25470025;N:29393 75       40767831 21026089 23298123 25470025 29393 ERX11852295 ERS17743544 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15112 15112 ERR12476454 ERX11852275 ERS17743538 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1210 from a cross with a fed father 1210 Fed 1210F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:184 277005 1210F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1210F_S7_L003_R1_001.fastq.gz fastq 100467804.0 1338769.0 ena RUN TAB 15 01 2024 21:42:36:184 277006 0:75.04 A:37096238;C:19156191;G:21628367;T:22539758;N:47250 75       37096238 19156191 21628367 22539758 47250 ERX11852275 ERS17743538 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15113 15113 ERR12476477 ERX11852298 ERS17743543 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a starved father 1242D Starved 1242SD   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:200 277051 1242SD 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242SD_S14_L002_R1_001.fastq.gz fastq 95483395.0 1269021.0 ena RUN TAB 15 01 2024 21:42:36:201 277052 0:75.24 A:33251808;C:18599068;G:20397415;T:23215065;N:20039 75       33251808 18599068 20397415 23215065 20039 ERX11852298 ERS17743543 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15114 15114 ERR12476443 ERX11852264 ERS17743535 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1118 from a cross with a starved father 1118 Starved 1118S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:176 276983 1118S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1118S_S10_L004_R1_001.fastq.gz fastq 88773312.0 1181250.0 ena RUN TAB 15 01 2024 21:42:36:177 276984 0:75.15 A:31460448;C:17120679;G:19117608;T:21054486;N:20091 75       31460448 17120679 19117608 21054486 20091 ERX11852264 ERS17743535 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15115 15115 ERR12476476 ERX11852297 ERS17743543 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a starved father 1242D Starved 1242SD   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:200 277049 1242SD 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242SD_S14_L001_R1_001.fastq.gz fastq 91072875.0 1210121.0 ena RUN TAB 15 01 2024 21:42:36:200 277050 0:75.26 A:31859074;C:17724212;G:19393637;T:22075784;N:20168 75       31859074 17724212 19393637 22075784 20168 ERX11852297 ERS17743543 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15116 15116 ERR12476463 ERX11852284 ERS17743540 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1219 from a cross with a fed father 1219 Fed 1219F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:190 277023 1219F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1219F_S11_L004_R1_001.fastq.gz fastq 96315015.0 1280935.0 ena RUN TAB 15 01 2024 21:42:36:191 277024 0:75.19 A:33841468;C:18744196;G:20803688;T:22906396;N:19267 75       33841468 18744196 20803688 22906396 19267 ERX11852284 ERS17743540 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15117 15117 ERR12476445 ERX11852266 ERS17743536 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1203 from a cross with a fed father 1203 Fed 1203F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:178 276987 1203F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1203F_S5_L002_R1_001.fastq.gz fastq 102458617.0 1363028.0 ena RUN TAB 15 01 2024 21:42:36:178 276988 0:75.17 A:36510957;C:19511996;G:22025384;T:24392965;N:17315 75       36510957 19511996 22025384 24392965 17315 ERX11852266 ERS17743536 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
16526 16526 ERR667398 ERX622886 ERS463339 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548493 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:43Z|External Id:SAMEA2548493|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:43Z|INSDC status:public|Submitter Id:50Cyclop 0 1EtOH 24hpf control 4 sc 1972462|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 0.1% v/v ethanol.A 8 base indexing sequence TCAGGAGG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:50Cyclop 0 1EtOH 24hpf control 4 sc 1972462|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#36 10517312 Illumina sequencing of library 10517312 constructed from sample accession ERS463339 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TCAGGAGG. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#36.cram cram 170828190.0 1314063.0 SC RUN 13256 1#36 0:55 1:75 A:44768263;C:34386047;G:35500778;T:56156162;N:16940 55 75     44768263 34386047 35500778 56156162 16940 ERX622886 ERS463339 ERA375333 SC Wellcome Sanger Institute 2 0.13166 0.8204 0.06755 0.19006 0.95753 0.81655 0.76236 0.68533 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16527 16527 ERR667397 ERX622885 ERS463338 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548492 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:41:34Z|External Id:SAMEA2548492|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:41:34Z|INSDC status:public|Submitter Id:50Cyclop 0 1EtOH 24hpf control 3 sc 1972461|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 0.1% v/v ethanol.A 8 base indexing sequence TCTCACGG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:50Cyclop 0 1EtOH 24hpf control 3 sc 1972461|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#35 10517311 Illumina sequencing of library 10517311 constructed from sample accession ERS463338 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TCTCACGG. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#35.cram cram 261820650.0 2014005.0 SC RUN 13256 1#35 0:55 1:75 A:72670470;C:50112031;G:54263310;T:84750983;N:23856 55 75     72670470 50112031 54263310 84750983 23856 ERX622885 ERS463338 ERA375333 SC Wellcome Sanger Institute 2 0.17465 0.75166 0.11391 0.1792 0.95937 0.84238 0.73795 0.70275 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16528 16528 ERR667396 ERX622884 ERS463337 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548491 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:17Z|External Id:SAMEA2548491|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:17Z|INSDC status:public|Submitter Id:50Cyclop 0 1EtOH 24hpf control 2 sc 1972460|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 0.1% v/v ethanol.A 8 base indexing sequence TACTTCGG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:50Cyclop 0 1EtOH 24hpf control 2 sc 1972460|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#34 10517310 Illumina sequencing of library 10517310 constructed from sample accession ERS463337 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TACTTCGG. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#34.cram cram 291378100.0 2241370.0 SC RUN 13256 1#34 0:55 1:75 A:80660045;C:56367784;G:60328044;T:93993547;N:28680 55 75     80660045 56367784 60328044 93993547 28680 ERX622884 ERS463337 ERA375333 SC Wellcome Sanger Institute 2 0.16274 0.76681 0.10005 0.16164 0.95994 0.84228 0.77601 0.72125 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16529 16529 ERR667395 ERX622883 ERS463336 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548490 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:43Z|External Id:SAMEA2548490|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:43Z|INSDC status:public|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 12 sc 1972459|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TGAACTGG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:50Cyclop 0 1EtOH 24hpf treated 12 sc 1972459|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#33 10517309 Illumina sequencing of library 10517309 constructed from sample accession ERS463336 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TGAACTGG. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#33.cram cram 159495050.0 1226885.0 SC RUN 13256 1#33 0:55 1:75 A:44526945;C:31107840;G:32400438;T:51444629;N:15198 55 75     44526945 31107840 32400438 51444629 15198 ERX622883 ERS463336 ERA375333 SC Wellcome Sanger Institute 2 0.14405 0.72387 0.09685 0.16934 0.96585 0.84476 0.75451 0.71348 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16530 16530 ERR667394 ERX622882 ERS463335 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548489 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:41:33Z|External Id:SAMEA2548489|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:41:33Z|INSDC status:public|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 11 sc 1972458|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TTGGTATG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:50Cyclop 0 1EtOH 24hpf treated 11 sc 1972458|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#32 10517308 Illumina sequencing of library 10517308 constructed from sample accession ERS463335 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TTGGTATG. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#32.cram cram 230733620.0 1774874.0 SC RUN 13256 1#32 0:55 1:75 A:65923552;C:43534910;G:44813128;T:76440148;N:21882 55 75     65923552 43534910 44813128 76440148 21882 ERX622882 ERS463335 ERA375333 SC Wellcome Sanger Institute 2 0.16493 0.71702 0.10319 0.16046 0.96035 0.83364 0.7605 0.69357 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16531 16531 ERR667393 ERX622881 ERS463334 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548488 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:17Z|External Id:SAMEA2548488|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:17Z|INSDC status:public|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 10 sc 1972457|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TAACGCTG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:50Cyclop 0 1EtOH 24hpf treated 10 sc 1972457|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#31 10517307 Illumina sequencing of library 10517307 constructed from sample accession ERS463334 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TAACGCTG. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#31.cram cram 169693940.0 1305338.0 SC RUN 13256 1#31 0:55 1:75 A:47216999;C:32233282;G:34303404;T:55924495;N:15760 55 75     47216999 32233282 34303404 55924495 15760 ERX622881 ERS463334 ERA375333 SC Wellcome Sanger Institute 2 0.15711 0.76441 0.09573 0.15362 0.96185 0.83625 0.78358 0.43248 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16532 16532 ERR667392 ERX622880 ERS463333 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548487 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:43Z|External Id:SAMEA2548487|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:43Z|INSDC status:public|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 9 sc 1972456|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TCGAAGTG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:50Cyclop 0 1EtOH 24hpf treated 9 sc 1972456|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#30 10517306 Illumina sequencing of library 10517306 constructed from sample accession ERS463333 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TCGAAGTG. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#30.cram cram 246126400.0 1893280.0 SC RUN 13256 1#30 0:55 1:75 A:64877434;C:48807745;G:51055789;T:81362490;N:22942 55 75     64877434 48807745 51055789 81362490 22942 ERX622880 ERS463333 ERA375333 SC Wellcome Sanger Institute 2 0.13616 0.81131 0.0854 0.19973 0.96556 0.82757 0.74775 0.70258 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16533 16533 ERR667391 ERX622879 ERS463332 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548486 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:41:33Z|External Id:SAMEA2548486|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:41:33Z|INSDC status:public|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 8 sc 1972455|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TTCCATTG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:50Cyclop 0 1EtOH 24hpf treated 8 sc 1972455|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#29 10517305 Illumina sequencing of library 10517305 constructed from sample accession ERS463332 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TTCCATTG. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#29.cram cram 237043690.0 1823413.0 SC RUN 13256 1#29 0:55 1:75 A:68761865;C:43795810;G:47113828;T:77348945;N:23242 55 75     68761865 43795810 47113828 77348945 23242 ERX622879 ERS463332 ERA375333 SC Wellcome Sanger Institute 2 0.13798 0.71442 0.08126 0.13596 0.95712 0.83751 0.72277 0.7226 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16534 16534 ERR667390 ERX622878 ERS463331 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548485 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:17Z|External Id:SAMEA2548485|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:17Z|INSDC status:public|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 7 sc 1972454|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TAGTCTTG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:50Cyclop 0 1EtOH 24hpf treated 7 sc 1972454|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#28 10517304 Illumina sequencing of library 10517304 constructed from sample accession ERS463331 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TAGTCTTG. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#28.cram cram 394343300.0 3033410.0 SC RUN 13256 1#28 0:55 1:75 A:111651222;C:75521035;G:80020655;T:127113022;N:37366 55 75     111651222 75521035 80020655 127113022 37366 ERX622878 ERS463331 ERA375333 SC Wellcome Sanger Institute 2 0.13408 0.74717 0.07471 0.14051 0.95958 0.83467 0.75125 0.70647 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16535 16535 ERR667389 ERX622877 ERS463330 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548484 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:43Z|External Id:SAMEA2548484|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:43Z|INSDC status:public|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 6 sc 1972453|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TGTGGTTG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:50Cyclop 0 1EtOH 24hpf treated 6 sc 1972453|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#27 10517303 Illumina sequencing of library 10517303 constructed from sample accession ERS463330 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TGTGGTTG. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#27.cram cram 284205350.0 2186195.0 SC RUN 13256 1#27 0:55 1:75 A:81760893;C:54722204;G:55386801;T:92306336;N:29116 55 75     81760893 54722204 55386801 92306336 29116 ERX622877 ERS463330 ERA375333 SC Wellcome Sanger Institute 2 0.15161 0.71556 0.08596 0.14319 0.95868 0.8392 0.77754 0.71796 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16536 16536 ERR667388 ERX622876 ERS463329 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548483 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:41:33Z|External Id:SAMEA2548483|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:41:33Z|INSDC status:public|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 5 sc 1972452|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TCCTCAAT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:50Cyclop 0 1EtOH 24hpf treated 5 sc 1972452|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#26 10517302 Illumina sequencing of library 10517302 constructed from sample accession ERS463329 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TCCTCAAT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#26.cram cram 330810350.0 2544695.0 SC RUN 13256 1#26 0:55 1:75 A:93408226;C:61812207;G:69176898;T:106383919;N:29100 55 75     93408226 61812207 69176898 106383919 29100 ERX622876 ERS463329 ERA375333 SC Wellcome Sanger Institute 2 0.13377 0.69577 0.07532 0.14875 0.95781 0.8383 0.72303 0.71175 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16537 16537 ERR667387 ERX622875 ERS463328 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548482 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:16Z|External Id:SAMEA2548482|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:16Z|INSDC status:public|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 4 sc 1972451|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TACAGGAT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:50Cyclop 0 1EtOH 24hpf treated 4 sc 1972451|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#25 10517301 Illumina sequencing of library 10517301 constructed from sample accession ERS463328 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TACAGGAT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#25.cram cram 474507020.0 3650054.0 SC RUN 13256 1#25 0:55 1:75 A:131496123;C:90613341;G:97290951;T:155059153;N:47452 55 75     131496123 90613341 97290951 155059153 47452 ERX622875 ERS463328 ERA375333 SC Wellcome Sanger Institute 2 0.13262 0.73888 0.07276 0.15006 0.96451 0.83479 0.78366 0.72049 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16550 16550 ERR667386 ERX622874 ERS463327 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548481 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:43Z|External Id:SAMEA2548481|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:43Z|INSDC status:public|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 3 sc 1972450|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TAGTGACT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:50Cyclop 0 1EtOH 24hpf treated 3 sc 1972450|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#24 10517300 Illumina sequencing of library 10517300 constructed from sample accession ERS463327 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TAGTGACT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#24.cram cram 296075650.0 2277505.0 SC RUN 13256 1#24 0:55 1:75 A:82935889;C:56062979;G:59762388;T:97286073;N:28321 55 75     82935889 56062979 59762388 97286073 28321 ERX622874 ERS463327 ERA375333 SC Wellcome Sanger Institute 2 0.1437 0.74103 0.08347 0.14393 0.96325 0.83684 0.81783 0.70771 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16551 16551 ERR667385 ERX622873 ERS463326 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548480 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:41:33Z|External Id:SAMEA2548480|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:41:33Z|INSDC status:public|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 2 sc 1972449|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TTCCTGCT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:50Cyclop 0 1EtOH 24hpf treated 2 sc 1972449|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#23 10517299 Illumina sequencing of library 10517299 constructed from sample accession ERS463326 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TTCCTGCT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#23.cram cram 443750710.0 3413467.0 SC RUN 13256 1#23 0:55 1:75 A:124952195;C:85586617;G:94833109;T:138341796;N:36993 55 75     124952195 85586617 94833109 138341796 36993 ERX622873 ERS463326 ERA375333 SC Wellcome Sanger Institute 2 0.15245 0.72135 0.07368 0.15151 0.95568 0.84449 0.77081 0.72424 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16552 16552 ERR667384 ERX622872 ERS463325 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548479 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:16Z|External Id:SAMEA2548479|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:16Z|INSDC status:public|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 1 sc 1972448|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TGCGATCT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:50Cyclop 0 1EtOH 24hpf treated 1 sc 1972448|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#22 10517298 Illumina sequencing of library 10517298 constructed from sample accession ERS463325 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TGCGATCT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#22.cram cram 298785370.0 2298349.0 SC RUN 13256 1#22 0:55 1:75 A:82163853;C:59663280;G:63342361;T:93589112;N:26764 55 75     82163853 59663280 63342361 93589112 26764 ERX622872 ERS463325 ERA375333 SC Wellcome Sanger Institute 2 0.13397 0.72614 0.07209 0.16108 0.96303 0.85188 0.78255 0.73973 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16553 16553 ERR667383 ERX622871 ERS463324 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548478 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:43Z|External Id:SAMEA2548478|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:43Z|INSDC status:public|Submitter Id:25Cyclop 05EtOH 24hpf control 12 sc 1972447|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TTGACTCT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:25Cyclop 05EtOH 24hpf control 12 sc 1972447|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#21 10517297 Illumina sequencing of library 10517297 constructed from sample accession ERS463324 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TTGACTCT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#21.cram cram 140774920.0 1082884.0 SC RUN 13256 1#21 0:55 1:75 A:39481115;C:27348433;G:30029240;T:43903005;N:13127 55 75     39481115 27348433 30029240 43903005 13127 ERX622871 ERS463324 ERA375333 SC Wellcome Sanger Institute 2 0.14879 0.72247 0.08143 0.15522 0.96118 0.84867 0.78965 0.74254 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16554 16554 ERR667382 ERX622870 ERS463323 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548477 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:41:33Z|External Id:SAMEA2548477|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:41:33Z|INSDC status:public|Submitter Id:25Cyclop 05EtOH 24hpf control 11 sc 1972446|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TGCATAGT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:25Cyclop 05EtOH 24hpf control 11 sc 1972446|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#20 10517296 Illumina sequencing of library 10517296 constructed from sample accession ERS463323 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TGCATAGT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#20.cram cram 178794590.0 1375343.0 SC RUN 13256 1#20 0:55 1:75 A:50890564;C:34618169;G:37008888;T:56258907;N:18062 55 75     50890564 34618169 37008888 56258907 18062 ERX622870 ERS463323 ERA375333 SC Wellcome Sanger Institute 2 0.15828 0.68013 0.10522 0.16411 0.96301 0.85147 0.77788 0.71946 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16555 16555 ERR667381 ERX622869 ERS463322 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548476 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:16Z|External Id:SAMEA2548476|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:16Z|INSDC status:public|Submitter Id:25Cyclop 05EtOH 24hpf control 10 sc 1972445|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TGATACGT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:25Cyclop 05EtOH 24hpf control 10 sc 1972445|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#19 10517295 Illumina sequencing of library 10517295 constructed from sample accession ERS463322 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TGATACGT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#19.cram cram 152796020.0 1175354.0 SC RUN 13256 1#19 0:55 1:75 A:43164178;C:28497500;G:30636978;T:50482443;N:14921 55 75     43164178 28497500 30636978 50482443 14921 ERX622869 ERS463322 ERA375333 SC Wellcome Sanger Institute 2 0.17338 0.74214 0.11412 0.17188 0.95954 0.83475 0.77599 0.69646 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16556 16556 ERR667380 ERX622868 ERS463321 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548475 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:43Z|External Id:SAMEA2548475|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:43Z|INSDC status:public|Submitter Id:25Cyclop 05EtOH 24hpf control 9 sc 1972444|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TCGAGCGT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:25Cyclop 05EtOH 24hpf control 9 sc 1972444|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#18 10517294 Illumina sequencing of library 10517294 constructed from sample accession ERS463321 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TCGAGCGT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#18.cram cram 246614290.0 1897033.0 SC RUN 13256 1#18 0:55 1:75 A:65847226;C:48649826;G:51891861;T:80201978;N:23399 55 75     65847226 48649826 51891861 80201978 23399 ERX622868 ERS463321 ERA375333 SC Wellcome Sanger Institute 2 0.12616 0.80609 0.07386 0.19379 0.96566 0.82942 0.80786 0.70582 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16557 16557 ERR667379 ERX622867 ERS463320 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548474 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:41:33Z|External Id:SAMEA2548474|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:41:33Z|INSDC status:public|Submitter Id:25Cyclop 05EtOH 24hpf control 8 sc 1972443|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TTGGAGGT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:25Cyclop 05EtOH 24hpf control 8 sc 1972443|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#17 10517293 Illumina sequencing of library 10517293 constructed from sample accession ERS463320 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TTGGAGGT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#17.cram cram 192037820.0 1477214.0 SC RUN 13256 1#17 0:55 1:75 A:52262399;C:38034317;G:39394465;T:62328424;N:18215 55 75     52262399 38034317 39394465 62328424 18215 ERX622867 ERS463320 ERA375333 SC Wellcome Sanger Institute 2 0.13419 0.77104 0.06619 0.15595 0.96234 0.83431 0.80856 0.7337 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16558 16558 ERR667378 ERX622866 ERS463319 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548473 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:16Z|External Id:SAMEA2548473|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:16Z|INSDC status:public|Submitter Id:25Cyclop 05EtOH 24hpf control 7 sc 1972442|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TCTGCTGT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:25Cyclop 05EtOH 24hpf control 7 sc 1972442|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#16 10517292 Illumina sequencing of library 10517292 constructed from sample accession ERS463319 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TCTGCTGT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#16.cram cram 131783210.0 1013717.0 SC RUN 13256 1#16 0:55 1:75 A:36740307;C:25906782;G:28184476;T:40940400;N:11245 55 75     36740307 25906782 28184476 40940400 11245 ERX622866 ERS463319 ERA375333 SC Wellcome Sanger Institute 2 0.1814 0.75096 0.0779 0.15257 0.94408 0.83615 0.73999 0.70358 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16559 16559 ERR667377 ERX622865 ERS463318 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548472 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:43Z|External Id:SAMEA2548472|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:43Z|INSDC status:public|Submitter Id:25Cyclop 05EtOH 24hpf control 6 sc 1972441|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TTCTGTGT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:25Cyclop 05EtOH 24hpf control 6 sc 1972441|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#15 10517291 Illumina sequencing of library 10517291 constructed from sample accession ERS463318 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TTCTGTGT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#15.cram cram 297275420.0 2286734.0 SC RUN 13256 1#15 0:55 1:75 A:80591742;C:58460335;G:62097495;T:96099260;N:26588 55 75     80591742 58460335 62097495 96099260 26588 ERX622865 ERS463318 ERA375333 SC Wellcome Sanger Institute 2 0.14856 0.79328 0.08045 0.18298 0.95388 0.82524 0.74068 0.69319 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16560 16560 ERR667376 ERX622864 ERS463317 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548471 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:41:33Z|External Id:SAMEA2548471|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:41:33Z|INSDC status:public|Submitter Id:25Cyclop 05EtOH 24hpf control 5 sc 1972440|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TGTACCTT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:25Cyclop 05EtOH 24hpf control 5 sc 1972440|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#14 10517290 Illumina sequencing of library 10517290 constructed from sample accession ERS463317 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TGTACCTT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#14.cram cram 242173750.0 1862875.0 SC RUN 13256 1#14 0:55 1:75 A:72439393;C:44966903;G:51788847;T:72956754;N:21853 55 75     72439393 44966903 51788847 72956754 21853 ERX622864 ERS463317 ERA375333 SC Wellcome Sanger Institute 2 0.13638 0.61957 0.09812 0.16019 0.97009 0.87127 0.57527 0.73119 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16561 16561 ERR667375 ERX622863 ERS463316 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548470 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:16Z|External Id:SAMEA2548470|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:16Z|INSDC status:public|Submitter Id:25Cyclop 05EtOH 24hpf control 4 sc 1972439|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TCCGTCTT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:25Cyclop 05EtOH 24hpf control 4 sc 1972439|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#13 10517289 Illumina sequencing of library 10517289 constructed from sample accession ERS463316 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TCCGTCTT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#13.cram cram 236289560.0 1817612.0 SC RUN 13256 1#13 0:55 1:75 A:65497839;C:45569980;G:50614556;T:74585065;N:22120 55 75     65497839 45569980 50614556 74585065 22120 ERX622863 ERS463316 ERA375333 SC Wellcome Sanger Institute 2 0.16763 0.7428 0.08432 0.16616 0.95217 0.83857 0.73569 0.69906 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16574 16574 ERR667374 ERX622862 ERS463315 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548469 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:43Z|External Id:SAMEA2548469|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:43Z|INSDC status:public|Submitter Id:25Cyclop 05EtOH 24hpf control 3 sc 1972438|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TAAGCGTT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:25Cyclop 05EtOH 24hpf control 3 sc 1972438|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#12 10517288 Illumina sequencing of library 10517288 constructed from sample accession ERS463315 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TAAGCGTT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#12.cram cram 381482400.0 2934480.0 SC RUN 13256 1#12 0:55 1:75 A:108129259;C:71762350;G:76804777;T:124748024;N:37990 55 75     108129259 71762350 76804777 124748024 37990 ERX622862 ERS463315 ERA375333 SC Wellcome Sanger Institute 2 0.15494 0.73749 0.08887 0.16382 0.95747 0.83211 0.76336 0.69077 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16575 16575 ERR667373 ERX622861 ERS463314 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548468 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:41:33Z|External Id:SAMEA2548468|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:41:33Z|INSDC status:public|Submitter Id:25Cyclop 05EtOH 24hpf control 2 sc 1972437|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TCTCGGTT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:25Cyclop 05EtOH 24hpf control 2 sc 1972437|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#11 10517287 Illumina sequencing of library 10517287 constructed from sample accession ERS463314 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TCTCGGTT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#11.cram cram 219975210.0 1692117.0 SC RUN 13256 1#11 0:55 1:75 A:62730862;C:43360964;G:45653286;T:68211390;N:18708 55 75     62730862 43360964 45653286 68211390 18708 ERX622861 ERS463314 ERA375333 SC Wellcome Sanger Institute 2 0.1335 0.67379 0.05402 0.14367 0.96319 0.84877 0.81344 0.7263 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16576 16576 ERR667372 ERX622860 ERS463313 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548467 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:05Z|External Id:SAMEA2548467|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:05Z|INSDC status:public|Submitter Id:25Cyclop 05EtOH 24hpf control 1 sc 1972436|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TGGTTGTT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:25Cyclop 05EtOH 24hpf control 1 sc 1972436|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#10 10517286 Illumina sequencing of library 10517286 constructed from sample accession ERS463313 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TGGTTGTT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#10.cram cram 289606330.0 2227741.0 SC RUN 13256 1#10 0:55 1:75 A:83619693;C:55715592;G:57603582;T:92639222;N:28241 55 75     83619693 55715592 57603582 92639222 28241 ERX622860 ERS463313 ERA375333 SC Wellcome Sanger Institute 2 0.14312 0.69479 0.08173 0.15101 0.96185 0.84439 0.78182 0.7265 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16577 16577 ERR667371 ERX622859 ERS463312 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548466 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:43Z|External Id:SAMEA2548466|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:43Z|INSDC status:public|Submitter Id:25Cyclop 05EtOH 24hpf treated 12 sc 1972435|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 25 micromolar cyclopamine in 05% v/v ethanol. A 8 base indexing sequence GATCAGCG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:25Cyclop 05EtOH 24hpf treated 12 sc 1972435|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#9 10517285 Illumina sequencing of library 10517285 constructed from sample accession ERS463312 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence GATCAGCG. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#9.cram cram 179568740.0 1381298.0 SC RUN 13256 1#9 0:55 1:75 A:48952176;C:34402129;G:36985871;T:59212722;N:15842 55 75     48952176 34402129 36985871 59212722 15842 ERX622859 ERS463312 ERA375333 SC Wellcome Sanger Institute 2 0.16345 0.77594 0.10069 0.16964 0.95864 0.83045 0.78521 0.7004 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16578 16578 ERR667370 ERX622858 ERS463311 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548465 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:04Z|ENA LAST UPDATE:2018 03 08T17:41:33Z|External Id:SAMEA2548465|INSDC center name:SC|INSDC first public:2014 11 04T16:19:04Z|INSDC last update:2018 03 08T17:41:33Z|INSDC status:public|Submitter Id:25Cyclop 05EtOH 24hpf treated 11 sc 1972434|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 25 micromolar cyclopamine in 05% v/v ethanol. A 8 base indexing sequence ACTTGATG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:25Cyclop 05EtOH 24hpf treated 11 sc 1972434|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#8 10517284 Illumina sequencing of library 10517284 constructed from sample accession ERS463311 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence ACTTGATG. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#8.cram cram 137020910.0 1054007.0 SC RUN 13256 1#8 0:55 1:75 A:38049625;C:26414574;G:28139253;T:44406481;N:10977 55 75     38049625 26414574 28139253 44406481 10977 ERX622858 ERS463311 ERA375333 SC Wellcome Sanger Institute 2 0.1402 0.74335 0.08322 0.1663 0.96268 0.84043 0.77733 0.71859 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16579 16579 ERR667369 ERX622857 ERS463310 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548464 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:05Z|External Id:SAMEA2548464|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:05Z|INSDC status:public|Submitter Id:25Cyclop 05EtOH 24hpf treated 10 sc 1972433|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 25 micromolar cyclopamine in 05% v/v ethanol. A 8 base indexing sequence CAGATCTG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:25Cyclop 05EtOH 24hpf treated 10 sc 1972433|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#7 10517283 Illumina sequencing of library 10517283 constructed from sample accession ERS463310 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence CAGATCTG. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#7.cram cram 198153410.0 1524257.0 SC RUN 13256 1#7 0:55 1:75 A:52670252;C:39254438;G:42385338;T:63824260;N:19122 55 75     52670252 39254438 42385338 63824260 19122 ERX622857 ERS463310 ERA375333 SC Wellcome Sanger Institute 2 0.12556 0.78468 0.07074 0.18847 0.964 0.83526 0.78795 0.71023 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16580 16580 ERR667368 ERX622856 ERS463309 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548463 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:43Z|External Id:SAMEA2548463|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:43Z|INSDC status:public|Submitter Id:25Cyclop 05EtOH 24hpf treated 9 sc 1972432|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 25 micromolar cyclopamine in 05% v/v ethanol. A 8 base indexing sequence GCCAATGT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:25Cyclop 05EtOH 24hpf treated 9 sc 1972432|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#6 10517282 Illumina sequencing of library 10517282 constructed from sample accession ERS463309 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence GCCAATGT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#6.cram cram 311861420.0 2398934.0 SC RUN 13256 1#6 0:55 1:75 A:83917355;C:60106233;G:64499135;T:103308448;N:30249 55 75     83917355 60106233 64499135 103308448 30249 ERX622856 ERS463309 ERA375333 SC Wellcome Sanger Institute 2 0.12297 0.80619 0.0593 0.15961 0.96234 0.82248 0.79929 0.70162 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16581 16581 ERR667367 ERX622855 ERS463308 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548462 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:41:33Z|External Id:SAMEA2548462|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:41:33Z|INSDC status:public|Submitter Id:25Cyclop 05EtOH 24hpf treated 8 sc 1972431|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 25 micromolar cyclopamine in 05% v/v ethanol. A 8 base indexing sequence ACAGTGGT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:25Cyclop 05EtOH 24hpf treated 8 sc 1972431|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#5 10517281 Illumina sequencing of library 10517281 constructed from sample accession ERS463308 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence ACAGTGGT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#5.cram cram 319355660.0 2456582.0 SC RUN 13256 1#5 0:55 1:75 A:84900314;C:64205253;G:67464229;T:102759467;N:26397 55 75     84900314 64205253 67464229 102759467 26397 ERX622855 ERS463308 ERA375333 SC Wellcome Sanger Institute 2 0.11383 0.78215 0.05838 0.17935 0.96619 0.83727 0.7861 0.72598 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16582 16582 ERR667366 ERX622854 ERS463307 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548461 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:05Z|External Id:SAMEA2548461|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:05Z|INSDC status:public|Submitter Id:25Cyclop 05EtOH 24hpf treated 7 sc 1972430|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 25 micromolar cyclopamine in 05% v/v ethanol. A 8 base indexing sequence TGACCACT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:25Cyclop 05EtOH 24hpf treated 7 sc 1972430|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#4 10517280 Illumina sequencing of library 10517280 constructed from sample accession ERS463307 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TGACCACT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#4.cram cram 354540160.0 2727232.0 SC RUN 13256 1#4 0:55 1:75 A:97757414;C:68003475;G:75993436;T:112753315;N:32520 55 75     97757414 68003475 75993436 112753315 32520 ERX622854 ERS463307 ERA375333 SC Wellcome Sanger Institute 2 0.12969 0.72947 0.07042 0.14757 0.9614 0.84017 0.78018 0.71871 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16583 16583 ERR667365 ERX622853 ERS463306 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548460 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:43Z|External Id:SAMEA2548460|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:43Z|INSDC status:public|Submitter Id:25Cyclop 05EtOH 24hpf treated 6 sc 1972429|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 25 micromolar cyclopamine in 05% v/v ethanol. A 8 base indexing sequence TTAGGCAT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:25Cyclop 05EtOH 24hpf treated 6 sc 1972429|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#3 10517279 Illumina sequencing of library 10517279 constructed from sample accession ERS463306 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TTAGGCAT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#3.cram cram 602820270.0 4637079.0 SC RUN 13256 1#3 0:55 1:75 A:165474925;C:115590273;G:123825630;T:197870518;N:58924 55 75     165474925 115590273 123825630 197870518 58924 ERX622853 ERS463306 ERA375333 SC Wellcome Sanger Institute 2 0.141 0.74407 0.08834 0.15443 0.96475 0.83958 0.78331 0.7194 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16584 16584 ERR667364 ERX622852 ERS463305 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548459 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:41:33Z|External Id:SAMEA2548459|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:41:33Z|INSDC status:public|Submitter Id:25Cyclop 05EtOH 24hpf treated 4 sc 1972428|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 25 micromolar cyclopamine in 05% v/v ethanol. A 8 base indexing sequence CGATGTTT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:25Cyclop 05EtOH 24hpf treated 4 sc 1972428|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#2 10517278 Illumina sequencing of library 10517278 constructed from sample accession ERS463305 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence CGATGTTT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#2.cram cram 192840440.0 1483388.0 SC RUN 13256 1#2 0:55 1:75 A:53469380;C:37747264;G:40238127;T:61365974;N:19695 55 75     53469380 37747264 40238127 61365974 19695 ERX622852 ERS463305 ERA375333 SC Wellcome Sanger Institute 2 0.14229 0.74015 0.07887 0.16243 0.96357 0.84687 0.7426 0.72806 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16585 16585 ERR667363 ERX622851 ERS463304 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548458 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:04Z|ENA LAST UPDATE:2018 03 08T17:42:05Z|External Id:SAMEA2548458|INSDC center name:SC|INSDC first public:2014 11 04T16:19:04Z|INSDC last update:2018 03 08T17:42:05Z|INSDC status:public|Submitter Id:25Cyclop 05EtOH 24hpf treated 3 sc 1972427|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 25 micromolar cyclopamine in 05% v/v ethanol. A 8 base indexing sequence ATCACGTT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:25Cyclop 05EtOH 24hpf treated 3 sc 1972427|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 1#1 10517277 Illumina sequencing of library 10517277 constructed from sample accession ERS463304 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence ATCACGTT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_1#1.cram cram 160035720.0 1231044.0 SC RUN 13256 1#1 0:55 1:75 A:44435310;C:30672417;G:33442253;T:51472358;N:13382 55 75     44435310 30672417 33442253 51472358 13382 ERX622851 ERS463304 ERA375333 SC Wellcome Sanger Institute 2 0.13712 0.73194 0.08578 0.14534 0.96617 0.8465 0.77185 0.72507 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16624 16624 ERR667516 ERX623004 ERS463380 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548534 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:41:35Z|External Id:SAMEA2548534|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:41:35Z|INSDC status:public|Submitter Id:Cyclop EtOH 24hpf untreated 12 sc 1972503|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo GCTCCTTG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:Cyclop EtOH 24hpf untreated 12 sc 1972503|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 2#77 10517353 Illumina sequencing of library 10517353 constructed from sample accession ERS463380 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 2. This submission includes reads tagged with the sequence GCTCCTTG. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_2#77.cram cram 249438020.0 1918754.0 SC RUN 13256 2#77 0:55 1:75 A:69145824;C:47578386;G:51851786;T:80816909;N:45115 55 75     69145824 47578386 51851786 80816909 45115 ERX623004 ERS463380 ERA375333 SC Wellcome Sanger Institute 2 0.16093 0.76664 0.10187 0.15638 0.95629 0.84127 0.71423 0.71239 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16625 16625 ERR667515 ERX623003 ERS463379 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548533 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:17Z|External Id:SAMEA2548533|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:17Z|INSDC status:public|Submitter Id:Cyclop EtOH 24hpf untreated 11 sc 1972502|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo GAGCCAAT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:Cyclop EtOH 24hpf untreated 11 sc 1972502|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 2#76 10517352 Illumina sequencing of library 10517352 constructed from sample accession ERS463379 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 2. This submission includes reads tagged with the sequence GAGCCAAT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_2#76.cram cram 170774240.0 1313648.0 SC RUN 13256 2#76 0:55 1:75 A:45646116;C:32502967;G:34986649;T:57607203;N:31305 55 75     45646116 32502967 34986649 57607203 31305 ERX623003 ERS463379 ERA375333 SC Wellcome Sanger Institute 2 0.14671 0.76516 0.0975 0.18223 0.96341 0.83007 0.75675 0.48594 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16626 16626 ERR667514 ERX623002 ERS463378 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548532 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:58Z|External Id:SAMEA2548532|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:58Z|INSDC status:public|Submitter Id:Cyclop EtOH 24hpf untreated 10 sc 1972501|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo GGAATGAT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:Cyclop EtOH 24hpf untreated 10 sc 1972501|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 2#75 10517351 Illumina sequencing of library 10517351 constructed from sample accession ERS463378 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 2. This submission includes reads tagged with the sequence GGAATGAT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_2#75.cram cram 220719590.0 1697843.0 SC RUN 13256 2#75 0:55 1:75 A:59911566;C:41292649;G:43822522;T:75650330;N:42523 55 75     59911566 41292649 43822522 75650330 42523 ERX623002 ERS463378 ERA375333 SC Wellcome Sanger Institute 2 0.16085 0.76121 0.10235 0.17156 0.96351 0.82901 0.8 0.67394 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16627 16627 ERR667513 ERX623001 ERS463377 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548531 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:41:35Z|External Id:SAMEA2548531|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:41:35Z|INSDC status:public|Submitter Id:Cyclop EtOH 24hpf untreated 9 sc 1972500|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo GTCGCTAT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:Cyclop EtOH 24hpf untreated 9 sc 1972500|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 2#74 10517350 Illumina sequencing of library 10517350 constructed from sample accession ERS463377 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 2. This submission includes reads tagged with the sequence GTCGCTAT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_2#74.cram cram 229666060.0 1766662.0 SC RUN 13256 2#74 0:55 1:75 A:63689398;C:43511689;G:47122878;T:75300451;N:41644 55 75     63689398 43511689 47122878 75300451 41644 ERX623001 ERS463377 ERA375333 SC Wellcome Sanger Institute 2 0.1466 0.75852 0.08129 0.14878 0.96057 0.83485 0.77591 0.70019 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
16628 16628 ERR667512 ERX623000 ERS463376 ERP008536 PRJEB7614 Screening zebrafish embryos treated with small molecules by transcriptome profiling Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.         SAMEA2548530 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 11 04T16:19:03Z|ENA LAST UPDATE:2018 03 08T17:42:17Z|External Id:SAMEA2548530|INSDC center name:SC|INSDC first public:2014 11 04T16:19:03Z|INSDC last update:2018 03 08T17:42:17Z|INSDC status:public|Submitter Id:Cyclop EtOH 24hpf untreated 8 sc 1972499|common name:zebrafish|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo GTTAGCCT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:Cyclop EtOH 24hpf untreated 8 sc 1972499|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 13256 2#73 10517349 Illumina sequencing of library 10517349 constructed from sample accession ERS463376 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 2. This submission includes reads tagged with the sequence GTTAGCCT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP008536 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2014 11 04|ENA LAST UPDATE:2018 11 16 13256_2#73.cram cram 224679650.0 1728305.0 SC RUN 13256 2#73 0:55 1:75 A:61542748;C:43621774;G:46869683;T:72605002;N:40443 55 75     61542748 43621774 46869683 72605002 40443 ERX623000 ERS463376 ERA375333 SC Wellcome Sanger Institute 2 0.17554 0.74212 0.0938 0.16223 0.96226 0.84378 0.7451 0.72448 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-11-04 Pharyngula Embryo Embryo Imprecise All anatomical structures

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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");;