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1,088 rows where devstage_curation = "Undetermined" and tissue_curation = "Undetermined"

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experiment.library_selection >10

technology 6

experiment.platform 5

experiment.library_strategy 5

devstage_curation_coarse 5

tissue_curation_coarse 2

experiment.library_source 2

experiment.library_layout 2

tissue_curation 1

  • Undetermined · 1,088 ✖

devstage_curation 1

  • Undetermined · 1,088 ✖
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
41 41 DRR408245 DRX393851 DRS407176 DRP012042 PRJDB14275 Zebrafish EN/ENCDC RNA seq DRP012042 Transcriptome Analysis A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.     zebrafish 5 day GFP positive enteric neurons replicate 3 zebrafish EN replicate 3 SAMD00529465   sample name:zebrafish EN replicate 3|biological replicate:eneteric neurons 3|strain:TgSAGFFLF219B; uas:gfp                 NextSeq 550 paired end sequencing of SAMD00529465 DRX393851 190326ENvsNC N703 5day;EntericNeuron;rep3 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012042 NextSeq 550 paired end sequencing of SAMD00529465       3729799291.0 23985772.0 DRR408245 0:77.75 1:77.75 A:978752781;C:879988139;G:903976580;T:962122970;N:4958821 77 77     978752781 879988139 903976580 962122970 4958821 DRX393851 DRS407176 DRA014886 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Japan 2024-09-22 Undetermined Larval Undetermined Undetermined
42 42 DRR408244 DRX393850 DRS407175 DRP012042 PRJDB14275 Zebrafish EN/ENCDC RNA seq DRP012042 Transcriptome Analysis A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.     zebrafish 5 day GFP positive enteric neurons replicate 2 zebrafish EN replicate 2 SAMD00529464   sample name:zebrafish EN replicate 2|biological replicate:eneteric neurons 2|strain:TgSAGFFLF218B; uas:gfp                 NextSeq 550 paired end sequencing of SAMD00529464 DRX393850 190326ENvsNC N702 5day;EntericNeuron;rep2 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012042 NextSeq 550 paired end sequencing of SAMD00529464       3315994810.0 21477755.0 DRR408244 0:77.19 1:77.20 A:873970427;C:778042505;G:798459853;T:859611841;N:5910184 77 77     873970427 778042505 798459853 859611841 5910184 DRX393850 DRS407175 DRA014886 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Japan 2024-09-22 Undetermined Larval Undetermined Undetermined
43 43 DRR408243 DRX393849 DRS407174 DRP012042 PRJDB14275 Zebrafish EN/ENCDC RNA seq DRP012042 Transcriptome Analysis A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.     zebrafish 5 day GFP positive enteric neurons replicate 1 zebrafish EN replicate 1 SAMD00529463   sample name:zebrafish EN replicate 1|biological replicate:eneteric neurons 1|strain:TgSAGFFLF217B; uas:gfp                 NextSeq 550 paired end sequencing of SAMD00529463 DRX393849 190326ENvsNC N701 5day;EntericNeuron;rep1 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012042 NextSeq 550 paired end sequencing of SAMD00529463       2999501518.0 19455440.0 DRR408243 0:77.08 1:77.09 A:788053541;C:705895776;G:724185148;T:775760738;N:5606315 77 77     788053541 705895776 724185148 775760738 5606315 DRX393849 DRS407174 DRA014886 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Japan 2024-09-22 Undetermined Larval Undetermined Undetermined
9337 9337 ERR2865439 ERX2871399 ERS2871019 ERP111778 PRJEB29472 RNAseq analysis of slbp mutants in Zebrafish ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14 Other Through forward genetic screening for mutations affecting visual system development we identified prominent coloboma and cell autonomous retinal neuron differentiation lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when and locations where post mitotic cells have differentiated in wild type siblings. Indeed RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated for instance in axon guidance that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise or promote transitions in cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes. ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01     sibling 3 SAMEA5059848 Department of Cell and Developmental Biology ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059848|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele sibling3|common name:zebrafish|sample name:ele sibling3|scientific name:Danio rerio                 Illumina HiSeq 3000 paired end sequencing ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 6 unspecified 1     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   ERP111778 Illumina HiSeq 3000 paired end sequencing ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16 ele_sib_F_CTTGTA_L004_R2_001.fastq.gz ele_sib_F_CTTGTA_L004_R1_001.fastq.gz fastq fastq 2823621200.0 14118106.0 ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 6 0:100 1:100 A:752781583;C:663838191;G:656422705;T:750213027;N:365694 100 100     752781583 663838191 656422705 750213027 365694 ERX2871399 ERS2871019 ERA1643817 Department of Cell and Developmental Biology|European Nucleotide Archive Department of Cell and Developmental Biology 2 0.95595 0.95486 0.09407 0.09431 0.67529 0.67673 0.45173 0.44515 100 100 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   Unknown 2018-11-01 Undetermined Embryo Undetermined Embryo Imprecise
9338 9338 ERR2865438 ERX2871398 ERS2871018 ERP111778 PRJEB29472 RNAseq analysis of slbp mutants in Zebrafish ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14 Other Through forward genetic screening for mutations affecting visual system development we identified prominent coloboma and cell autonomous retinal neuron differentiation lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when and locations where post mitotic cells have differentiated in wild type siblings. Indeed RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated for instance in axon guidance that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise or promote transitions in cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes. ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01     sibling 2 SAMEA5059847 Department of Cell and Developmental Biology ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059847|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele sibling2|common name:zebrafish|sample name:ele sibling2|scientific name:Danio rerio                 Illumina HiSeq 3000 paired end sequencing ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 5 unspecified 1     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   ERP111778 Illumina HiSeq 3000 paired end sequencing ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16 ele_sib_D_GCCAAT_L004_R1_001.fastq.gz ele_sib_D_GCCAAT_L004_R2_001.fastq.gz fastq fastq 4217962600.0 21089813.0 ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 5 0:100 1:100 A:1119324653;C:996982862;G:984906708;T:1116209552;N:538825 100 100     1119324653 996982862 984906708 1116209552 538825 ERX2871398 ERS2871018 ERA1643817 Department of Cell and Developmental Biology|European Nucleotide Archive Department of Cell and Developmental Biology 2 0.95341 0.95274 0.09215 0.09238 0.67296 0.67493 0.46185 0.4648 100 100 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   Unknown 2018-11-01 Undetermined Embryo Undetermined Embryo Imprecise
9339 9339 ERR2865437 ERX2871397 ERS2871017 ERP111778 PRJEB29472 RNAseq analysis of slbp mutants in Zebrafish ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14 Other Through forward genetic screening for mutations affecting visual system development we identified prominent coloboma and cell autonomous retinal neuron differentiation lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when and locations where post mitotic cells have differentiated in wild type siblings. Indeed RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated for instance in axon guidance that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise or promote transitions in cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes. ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01     sibling 1 SAMEA5059846 Department of Cell and Developmental Biology ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059846|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele sibling1|common name:zebrafish|sample name:ele sibling1|scientific name:Danio rerio                 Illumina HiSeq 3000 paired end sequencing ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 4 unspecified 1     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   ERP111778 Illumina HiSeq 3000 paired end sequencing ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16 ele_sib_B_TGACCA_L004_R1_001.fastq.gz ele_sib_B_TGACCA_L004_R2_001.fastq.gz fastq fastq 5241628000.0 26208140.0 ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 4 0:100 1:100 A:1393802799;C:1235804455;G:1219328189;T:1392021956;N:670601 100 100     1393802799 1235804455 1219328189 1392021956 670601 ERX2871397 ERS2871017 ERA1643817 Department of Cell and Developmental Biology|European Nucleotide Archive Department of Cell and Developmental Biology 2 0.95296 0.95133 0.10275 0.1028 0.67018 0.67146 0.46488 0.46482 100 100 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   Unknown 2018-11-01 Undetermined Embryo Undetermined Embryo Imprecise
9340 9340 ERR2865436 ERX2871396 ERS2871016 ERP111778 PRJEB29472 RNAseq analysis of slbp mutants in Zebrafish ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14 Other Through forward genetic screening for mutations affecting visual system development we identified prominent coloboma and cell autonomous retinal neuron differentiation lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when and locations where post mitotic cells have differentiated in wild type siblings. Indeed RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated for instance in axon guidance that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise or promote transitions in cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes. ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01     mutant3 SAMEA5059845 Department of Cell and Developmental Biology ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059845|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele mutant3|common name:zebrafish|sample name:ele mutant3|scientific name:Danio rerio                 Illumina HiSeq 3000 paired end sequencing ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 3 unspecified 1     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   ERP111778 Illumina HiSeq 3000 paired end sequencing ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16 ele_E_CAGATC_L004_R1_001.fastq.gz ele_E_CAGATC_L004_R2_001.fastq.gz fastq fastq 3529752000.0 17648760.0 ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 3 0:100 1:100 A:933354224;C:837396695;G:828677816;T:929860782;N:462483 100 100     933354224 837396695 828677816 929860782 462483 ERX2871396 ERS2871016 ERA1643817 Department of Cell and Developmental Biology|European Nucleotide Archive Department of Cell and Developmental Biology 2 0.95621 0.95302 0.08584 0.08536 0.67048 0.67146 0.46615 0.46682 100 100 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   Unknown 2018-11-01 Undetermined Embryo Undetermined Embryo Imprecise
9341 9341 ERR2865435 ERX2871395 ERS2871015 ERP111778 PRJEB29472 RNAseq analysis of slbp mutants in Zebrafish ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14 Other Through forward genetic screening for mutations affecting visual system development we identified prominent coloboma and cell autonomous retinal neuron differentiation lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when and locations where post mitotic cells have differentiated in wild type siblings. Indeed RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated for instance in axon guidance that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise or promote transitions in cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes. ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01     mutant2 SAMEA5059844 Department of Cell and Developmental Biology ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059844|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele mutant2|common name:zebrafish|sample name:ele mutant2|scientific name:Danio rerio                 Illumina HiSeq 3000 paired end sequencing ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   ERP111778 Illumina HiSeq 3000 paired end sequencing ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16 ele_C_ACAGTG_L004_R1_001.fastq.gz ele_C_ACAGTG_L004_R2_001.fastq.gz fastq fastq 3119723800.0 15598619.0 ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 2 0:100 1:100 A:828335602;C:736691663;G:727853394;T:826449133;N:394008 100 100     828335602 736691663 727853394 826449133 394008 ERX2871395 ERS2871015 ERA1643817 Department of Cell and Developmental Biology|European Nucleotide Archive Department of Cell and Developmental Biology 2 0.94967 0.94864 0.0992 0.09955 0.65928 0.66014 0.47042 0.46835 100 100 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   Unknown 2018-11-01 Undetermined Embryo Undetermined Embryo Imprecise
9342 9342 ERR2865434 ERX2871394 ERS2871014 ERP111778 PRJEB29472 RNAseq analysis of slbp mutants in Zebrafish ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14 Other Through forward genetic screening for mutations affecting visual system development we identified prominent coloboma and cell autonomous retinal neuron differentiation lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when and locations where post mitotic cells have differentiated in wild type siblings. Indeed RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated for instance in axon guidance that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise or promote transitions in cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes. ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01     mutant1 SAMEA5059843 Department of Cell and Developmental Biology ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059843|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele mutant1|common name:zebrafish|sample name:ele mutant1|scientific name:Danio rerio                 Illumina HiSeq 3000 paired end sequencing ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:716 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   ERP111778 Illumina HiSeq 3000 paired end sequencing ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16 ele_A_CGATGT_L004_R1_001.fastq.gz ele_A_CGATGT_L004_R2_001.fastq.gz fastq fastq 2181939600.0 10909698.0 ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 1 0:100 1:100 A:578028200;C:516249107;G:510965740;T:576417363;N:279190 100 100     578028200 516249107 510965740 576417363 279190 ERX2871394 ERS2871014 ERA1643817 Department of Cell and Developmental Biology|European Nucleotide Archive Department of Cell and Developmental Biology 2 0.94968 0.94939 0.1131 0.11293 0.66245 0.66251 0.46654 0.47475 100 100 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   Unknown 2018-11-01 Undetermined Embryo Undetermined Embryo Imprecise
9918 9918 ERR5059480 ERX4865549 ERS5523939 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05     aAM 6h rep1 JD AD30 PRPN1970901   ENA FIRST PUBLIC:2022 07 05T12:06:33Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:33Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 01 2021 19:50:56:183 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-AD30_PRPN197090.tar.gz nanopore 3739882337.0 3148027.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 09 01 2021 19:50:56:183 1 0:1188.01 A:1054501690;C:834193435;G:847423060;T:1003764152;N:0 1188       1054501690 834193435 847423060 1003764152 0 ERX4865549 ERS5523939 ERA3206712 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       B   usable mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9920 9920 ERR4330695 ERX4277529 ERS4811113 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 2h rep1 WT 2h rep1 SAMEA7050483 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7050483|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD B2 PDBN005727|common name:zebrafish|sample name:JD B2 PDBN005727                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-B2_PDBN005727.tar.gz fastq     ena RUN CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 1                       ERX4277529   ERA2767154 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                             ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9921 9921 ERR4327134 ERX4273968 ERS4808634 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 4h rep2 WT 4h rep2 SAMEA7048000 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7048000|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD AM39 PDBN042841|common name:zebrafish|sample name:JD AM39 PDBN042841                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-AM39_PDBN042841.tar.gz nanopore 719646261.0 897768.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 1 0:801.59 A:210217908;C:152963718;G:157393834;T:199070801;N:0 801       210217908 152963718 157393834 199070801 0 ERX4273968 ERS4808634 ERA2764800 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   under 1.2% mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9922 9922 ERR4330696 ERX4277530 ERS4811114 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 4h rep1 WT 4h rep1 JD C3 PDBN006177   ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-C3_PDBN006177.tar.gz nanopore 4240799932.0 4331689.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 2 0:979.02 A:1229803846;C:914476674;G:943703560;T:1152815852;N:0 979       1229803846 914476674 943703560 1152815852 0 ERX4277530 ERS4811114 ERA2767154 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       B   usable mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9923 9923 ERR4327135 ERX4273969 ERS4808635 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 6h rep1 WT 6h rep1 JD AC29 PDBN024889   ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-AC29_PDBN024889.tar.gz nanopore 1900324756.0 2013035.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 2 0:944.01 A:549431032;C:411510218;G:422103800;T:517279706;N:0 944       549431032 411510218 422103800 517279706 0 ERX4273969 ERS4808635 ERA2764800 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   long read ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9924 9924 ERR4326350 ERX4273208 ERS4808398 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   430 LNA 6h rep1 430 LNA 6h rep1 SAMEA7047764 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7047764|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD H8 PDBN059569|common name:zebrafish|sample name:JD H8 PDBN059569                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 10:25:22:388 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-H8_PDBN059569.tar.gz nanopore 722817654.0 657296.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 10:25:22:388 1 0:1099.68 A:206996491;C:157022109;G:155085437;T:203713617;N:0 1099       206996491 157022109 155085437 203713617 0 ERX4273208 ERS4808398 ERA2764399 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   under 1.2% mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9925 9925 ERR4335436 ERX4282181 ERS4818366 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 6h rep2 WT 6h rep2 JD W23 PRPN039928   ENA FIRST PUBLIC:2022 07 05T12:06:24Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:24Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 13 07 2020 18:19:23:456 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-W23_PRPN039928.tar.gz nanopore 1268761319.0 1385621.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 13 07 2020 18:19:23:457 1 0:915.66 A:366823862;C:275507684;G:284634548;T:341795225;N:0 915       366823862 275507684 284634548 341795225 0 ERX4282181 ERS4818366 ERA2769006 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   under 1.2% mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9926 9926 ERR4321680 ERX4268538 ERS4808125 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 0h rep1 WT 0h rep1 JD A1 GDDN003032   ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 GridION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 06 07 2020 17:45:26:236 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE GridION   ERP122761 GridION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-A1_GDDN003032.tar.gz nanopore 753417826.0 698774.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 06 07 2020 17:45:26:236 1 0:1078.20 A:214525685;C:165042952;G:171160615;T:202688574;N:0 1078       214525685 165042952 171160615 202688574 0 ERX4268538 ERS4808125 ERA2763718 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   long read ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
10383 10383 ERR8517249 ERX8083723 ERS10517669 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 Modifier control hnRNPK 003 SAMEA12918519 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918519|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:hnRNPK 003|common name:zebrafish|sample name:hnRNPK 003                 NextSeq 500 paired end sequencing; Raw reads: hnRNPK 003 webin reads hnRNPK 003   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: hnRNPK 003 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 hnRNPK_003_R1.fastq.gz hnRNPK_003_R2.fastq.gz fastq fastq 2931486932.0 19421721.0 webin reads hnRNPK 003 0:75.51 1:75.43 A:759548162;C:700272829;G:700149526;T:770783019;N:733396 75 75     759548162 700272829 700149526 770783019 733396 ERX8083723 ERS10517669 ERA8937191 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.9621 0.96378 0.06994 0.06876 0.68757 0.68998 0.46746 0.47041 76 75 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
10384 10384 ERR8517226 ERX8083700 ERS10517665 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 Modifier control hnRNPK 001 SAMEA12918515 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918515|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:hnRNPK 001|common name:zebrafish|sample name:hnRNPK 001                 NextSeq 500 paired end sequencing; Raw reads: hnRNPK 001 webin reads hnRNPK 001   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: hnRNPK 001 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 hnRNPK_001_R1.fastq.gz hnRNPK_001_R2.fastq.gz fastq fastq 2728299749.0 18074835.0 webin reads hnRNPK 001 0:75.51 1:75.43 A:710869412;C:649804308;G:644363972;T:722599378;N:662679 75 75     710869412 649804308 644363972 722599378 662679 ERX8083700 ERS10517665 ERA8936710 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.96092 0.96336 0.07296 0.07144 0.68862 0.69209 0.47036 0.47104 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
10385 10385 ERR8517194 ERX8083668 ERS10517668 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 RNA control GFP 003 SAMEA12918518 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918518|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:GFP 003|common name:zebrafish|sample name:GFP 003                 NextSeq 500 paired end sequencing; Raw reads: GFP 003 webin reads GFP 003   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: GFP 003 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 GFP_003_R1.fastq.gz GFP_003_R2.fastq.gz fastq fastq 2845571506.0 18850866.0 webin reads GFP 003 0:75.52 1:75.43 A:737412560;C:678774596;G:684567775;T:744108157;N:708418 75 75     737412560 678774596 684567775 744108157 708418 ERX8083668 ERS10517668 ERA8936242 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.96279 0.96355 0.06774 0.06607 0.68864 0.69183 0.469 0.46906 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
10386 10386 ERR8517159 ERX8083633 ERS10517664 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 RNA control GFP 001 SAMEA12918514 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918514|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:GFP 001|common name:zebrafish|sample name:GFP 001                 NextSeq 500 paired end sequencing; Raw reads: GFP 001 webin reads GFP 001   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: GFP 001 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 GFP_001_R1.fastq.gz GFP_001_R2.fastq.gz fastq fastq 2873485447.0 19035162.0 webin reads GFP 001 0:75.52 1:75.44 A:746120172;C:687054955;G:682142981;T:757435799;N:731540 75 75     746120172 687054955 682142981 757435799 731540 ERX8083633 ERS10517664 ERA8935703 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.96176 0.96461 0.07014 0.06932 0.68672 0.68913 0.47006 0.46794 75 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
10387 10387 ERR8517115 ERX8083589 ERS10517671 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 Modifier rescue 91S hnRNPK 003 SAMEA12918521 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918521|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S hnRNPK 003|common name:zebrafish|sample name:91S hnRNPK 003                 NextSeq 500 paired end sequencing; Raw reads: 91S hnRNPK 003 webin reads 91S hnRNPK 003   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: 91S hnRNPK 003 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 91S_hnRNPK_003_R1.fastq.gz 91S_hnRNPK_003_R2.fastq.gz fastq fastq 2853403405.0 18902398.0 webin reads 91S hnRNPK 003 0:75.52 1:75.44 A:739541111;C:681340573;G:681790014;T:750013318;N:718389 75 75     739541111 681340573 681790014 750013318 718389 ERX8083589 ERS10517671 ERA8935191 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.96234 0.96429 0.0679 0.06627 0.68984 0.69126 0.46434 0.47087 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
10388 10388 ERR8517082 ERX8083556 ERS10517667 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 Modifier rescue 91S hnRNPK 001 SAMEA12918517 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918517|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S hnRNPK 001|common name:zebrafish|sample name:91S hnRNPK 001                 NextSeq 500 paired end sequencing; Raw reads: 91S hnRNPK 001 webin reads 91S hnRNPK 001   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: 91S hnRNPK 001 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 91S_hnRNPK_001_R1.fastq.gz 91S_hnRNPK_001_R2.fastq.gz fastq fastq 2795603091.0 18519699.0 webin reads 91S hnRNPK 001 0:75.52 1:75.43 A:722724564;C:672552332;G:664566386;T:735058575;N:701234 75 75     722724564 672552332 664566386 735058575 701234 ERX8083556 ERS10517667 ERA8934579 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.96307 0.96547 0.06551 0.06458 0.68714 0.68856 0.46817 0.46555 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
10389 10389 ERR8517039 ERX8083513 ERS10517670 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 Toxic condition 91S GFP 003 SAMEA12918520 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918520|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S GFP 003|common name:zebrafish|sample name:91S GFP 003                 NextSeq 500 paired end sequencing; Raw reads: 91S GFP 003 webin reads 91S GFP 003   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: 91S GFP 003 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 91S_GFP_003_R1.fastq.gz 91S_GFP_003_R2.fastq.gz fastq fastq 2946600193.0 19521826.0 webin reads 91S GFP 003 0:75.51 1:75.43 A:763284580;C:704439363;G:702989767;T:775149110;N:737373 75 75     763284580 704439363 702989767 775149110 737373 ERX8083513 ERS10517670 ERA8933888 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.96151 0.96295 0.06621 0.06481 0.68807 0.69092 0.46928 0.46982 75 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
10390 10390 ERR8516998 ERX8083472 ERS10517666 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 Toxic condition 91S GFP 001 SAMEA12918516 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918516|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S GFP 001|common name:zebrafish|sample name:91S GFP 001                 NextSeq 500 paired end sequencing; Raw reads: 91S GFP 001 webin reads 91S GFP 001   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: 91S GFP 001 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 91S_GFP_001_R1.fastq.gz 91S_GFP_001_R2.fastq.gz fastq fastq 2821113913.0 18686946.0 webin reads 91S GFP 001 0:75.52 1:75.44 A:726676187;C:676899384;G:676400816;T:740427303;N:710223 75 75     726676187 676899384 676400816 740427303 710223 ERX8083472 ERS10517666 ERA8933211 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.96147 0.96465 0.07106 0.06991 0.68822 0.69556 0.47261 0.47451 75 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
14875 14875 ERR12071836 ERX11454461 ERS16387703 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E115 1 SAMEA114399011 University of East Anglia ENA FIRST PUBLIC:2023 10 06T08:31:44Z|ENA LAST UPDATE:2023 10 06T08:31:44Z|External Id:SAMEA114399011|INSDC center name:University of East Anglia|INSDC first public:2023 10 06T08:31:44Z|INSDC last update:2023 10 06T08:31:44Z|INSDC status:public|Submitter Id:115 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:115 1|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:295 66715 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 10 06|ENA LAST UPDATE:2023 10 06 115-1_S69_L006_R1_001.fastq.gz 115-1_S69_L006_R2_001.fastq.gz fastq fastq 12813280704.0 50846352.0 ena RUN TAB 21 09 2023 13:32:15:295 66716 0:126 1:126 A:2451295493;C:3891843753;G:4001866488;T:2448421880;N:19853090 126 126     2451295493 3891843753 4001866488 2448421880 19853090 ERX11454461 ERS16387703 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.89907 0.8514 0.17845 0.173 0.80369 0.81085 0.83252 0.83449 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14876 14876 ERR12071855 ERX11454480 ERS16387722 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E83 5 SAMEA114399030 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:83 5|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:83 5|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:300 66753 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 83-5_S40_L008_R1_001.fastq.gz 83-5_S40_L008_R2_001.fastq.gz fastq fastq 13683493656.0 54299578.0 ena RUN TAB 21 09 2023 13:32:15:300 66754 0:126 1:126 A:2772843483;C:4073415925;G:4192640412;T:2641952920;N:2640916 126 126     2772843483 4073415925 4192640412 2641952920 2640916 ERX11454480 ERS16387722 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.92452 0.92427 0.15846 0.16251 0.7777 0.77666 0.78362 0.77515 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14877 14877 ERR12071854 ERX11454479 ERS16387721 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E83 4 SAMEA114399029 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:83 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:83 4|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:299 66751 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 83-4_S8_L002_R1_001.fastq.gz 83-4_S8_L002_R2_001.fastq.gz fastq fastq 10045714644.0 39863947.0 ena RUN TAB 21 09 2023 13:32:15:300 66752 0:126 1:126 A:2037388456;C:2963530056;G:3069663461;T:1972981871;N:2150800 126 126     2037388456 2963530056 3069663461 1972981871 2150800 ERX11454479 ERS16387721 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.91872 0.91762 0.16049 0.16307 0.76516 0.76644 0.77023 0.77199 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14878 14878 ERR12071853 ERX11454478 ERS16387720 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E83 3 SAMEA114399028 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:83 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:83 3|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:299 66749 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 83-3_S12_L003_R1_001.fastq.gz 83-3_S12_L003_R2_001.fastq.gz fastq fastq 17333567748.0 68783999.0 ena RUN TAB 21 09 2023 13:32:15:299 66750 0:126 1:126 A:3399006637;C:5245167754;G:5416988818;T:3269621086;N:2783453 126 126     3399006637 5245167754 5416988818 3269621086 2783453 ERX11454478 ERS16387720 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.93044 0.93099 0.14459 0.1479 0.77287 0.774 0.78248 0.78348 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14879 14879 ERR12071852 ERX11454477 ERS16387719 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E83 1 SAMEA114399027 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:83 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:83 1|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:299 66747 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 83-1_S4_L001_R1_001.fastq.gz 83-1_S4_L001_R2_001.fastq.gz fastq fastq 14977164132.0 59433191.0 ena RUN TAB 21 09 2023 13:32:15:299 66748 0:126 1:126 A:3115980365;C:4357431505;G:4531888641;T:2968758582;N:3105039 126 126     3115980365 4357431505 4531888641 2968758582 3105039 ERX11454477 ERS16387719 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.89622 0.89549 0.15698 0.16074 0.76558 0.76779 0.70301 0.73129 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14880 14880 ERR12071851 ERX11454476 ERS16387718 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E82 5 SAMEA114399026 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:82 5|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:82 5|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:299 66745 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 82-5_S3_L001_R1_001.fastq.gz 82-5_S3_L001_R2_001.fastq.gz fastq fastq 14575744764.0 57840257.0 ena RUN TAB 21 09 2023 13:32:15:299 66746 0:126 1:126 A:3079286238;C:4161280385;G:4315514217;T:3016549159;N:3114765 126 126     3079286238 4161280385 4315514217 3016549159 3114765 ERX11454476 ERS16387718 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.82553 0.82489 0.15941 0.16124 0.77337 0.77518 0.73773 0.75718 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14881 14881 ERR12071850 ERX11454475 ERS16387717 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E82 3 SAMEA114399025 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:82 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:82 3|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:298 66743 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 82-3_S11_L003_R1_001.fastq.gz 82-3_S11_L003_R2_001.fastq.gz fastq fastq 15753924144.0 62515572.0 ena RUN TAB 21 09 2023 13:32:15:299 66744 0:126 1:126 A:3294606329;C:4538635184;G:4708756438;T:3209425450;N:2500743 126 126     3294606329 4538635184 4708756438 3209425450 2500743 ERX11454475 ERS16387717 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.8642 0.86388 0.1596 0.16298 0.77051 0.77297 0.7599 0.7352 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14882 14882 ERR12071849 ERX11454474 ERS16387716 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E82 2 SAMEA114399024 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:82 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:82 2|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:298 66741 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 22 82-2_S7_L002_R1_001.fastq.gz 82-2_S7_L002_R2_001.fastq.gz fastq fastq 20680686684.0 82066217.0 ena RUN TAB 21 09 2023 13:32:15:298 66742 0:126 1:126 A:4358995918;C:5919331822;G:6101024757;T:4296885228;N:4448959 126 126     4358995918 5919331822 6101024757 4296885228 4448959 ERX11454474 ERS16387716 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.88722 0.88591 0.1721 0.1755 0.76207 0.76394 0.74661 0.7483 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14883 14883 ERR12071848 ERX11454473 ERS16387715 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E82 1 SAMEA114399023 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:82 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:82 1|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:298 66739 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 82-1_S39_L008_R1_001.fastq.gz 82-1_S39_L008_R2_001.fastq.gz fastq fastq 19062862812.0 75646281.0 ena RUN TAB 21 09 2023 13:32:15:298 66740 0:126 1:126 A:4015412618;C:5485657253;G:5643544062;T:3914646370;N:3602509 126 126     4015412618 5485657253 5643544062 3914646370 3602509 ERX11454473 ERS16387715 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.82331 0.82289 0.14959 0.15262 0.77786 0.77368 0.75014 0.71846 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14884 14884 ERR12071847 ERX11454472 ERS16387714 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E81 5 SAMEA114399022 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:81 5|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:81 5|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:298 66737 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 81-5_S6_L002_R1_001.fastq.gz 81-5_S6_L002_R2_001.fastq.gz fastq fastq 14105505960.0 55974230.0 ena RUN TAB 21 09 2023 13:32:15:298 66738 0:126 1:126 A:2867593807;C:4154280778;G:4295901883;T:2784713422;N:3016070 126 126     2867593807 4154280778 4295901883 2784713422 3016070 ERX11454472 ERS16387714 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.89055 0.89059 0.15225 0.15462 0.77031 0.7709 0.77204 0.74565 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14885 14885 ERR12071846 ERX11454471 ERS16387713 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E81 4 SAMEA114399021 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:81 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:81 4|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:297 66735 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 81-4_S38_L008_R1_001.fastq.gz 81-4_S38_L008_R2_001.fastq.gz fastq fastq 14056344540.0 55779145.0 ena RUN TAB 21 09 2023 13:32:15:298 66736 0:126 1:126 A:2941182079;C:4065026103;G:4178339299;T:2869101906;N:2695153 126 126     2941182079 4065026103 4178339299 2869101906 2695153 ERX11454471 ERS16387713 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.85089 0.84987 0.16263 0.16502 0.77837 0.77283 0.74931 0.72487 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14886 14886 ERR12071845 ERX11454470 ERS16387712 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E81 2 SAMEA114399020 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:81 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:81 2|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:297 66733 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 81-2_S10_L003_R2_001.fastq.gz 81-2_S10_L003_R1_001.fastq.gz fastq fastq 12344567004.0 48986377.0 ena RUN TAB 21 09 2023 13:32:15:297 66734 0:126 1:126 A:2564870489;C:3577715066;G:3699995887;T:2500054422;N:1931140 126 126     2564870489 3577715066 3699995887 2500054422 1931140 ERX11454470 ERS16387712 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.81332 0.81278 0.14345 0.14595 0.77962 0.78011 0.77642 0.76714 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14887 14887 ERR12071844 ERX11454469 ERS16387711 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E81 1 SAMEA114399019 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:81 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:81 1|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:297 66731 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 81-1_S2_L001_R1_001.fastq.gz 81-1_S2_L001_R2_001.fastq.gz fastq fastq 16863847056.0 66920028.0 ena RUN TAB 21 09 2023 13:32:15:297 66732 0:126 1:126 A:3484102096;C:4908704805;G:5083802657;T:3383595635;N:3641863 126 126     3484102096 4908704805 5083802657 3383595635 3641863 ERX11454469 ERS16387711 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.90019 0.89959 0.16463 0.16683 0.76607 0.76792 0.76365 0.73132 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14888 14888 ERR12071843 ERX11454468 ERS16387710 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E80 4 SAMEA114399018 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:80 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:80 4|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:297 66729 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 80-4_S9_L003_R1_001.fastq.gz 80-4_S9_L003_R2_001.fastq.gz fastq fastq 22230539604.0 88216427.0 ena RUN TAB 21 09 2023 13:32:15:297 66730 0:126 1:126 A:4399600032;C:6651638899;G:6855034908;T:4320719496;N:3546269 126 126     4399600032 6651638899 6855034908 4320719496 3546269 ERX11454468 ERS16387710 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.84585 0.84448 0.14327 0.14586 0.79078 0.79251 0.79803 0.79459 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14889 14889 ERR12071842 ERX11454467 ERS16387709 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E80 3 SAMEA114399017 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:80 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:80 3|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:296 66727 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 80-3_S1_L001_R2_001.fastq.gz 80-3_S1_L001_R1_001.fastq.gz fastq fastq 17944230024.0 71207262.0 ena RUN TAB 21 09 2023 13:32:15:296 66728 0:126 1:126 A:3713490828;C:5207225554;G:5378396527;T:3641393155;N:3723960 126 126     3713490828 5207225554 5378396527 3641393155 3723960 ERX11454467 ERS16387709 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.84454 0.84386 0.14922 0.15129 0.77264 0.77339 0.75797 0.76206 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14890 14890 ERR12071841 ERX11454466 ERS16387708 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E80 2 SAMEA114399016 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:80 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:80 2|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:296 66725 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 80-2_S5_L002_R1_001.fastq.gz 80-2_S5_L002_R2_001.fastq.gz fastq fastq 16641238320.0 66036660.0 ena RUN TAB 21 09 2023 13:32:15:296 66726 0:126 1:126 A:3508280857;C:4757668643;G:4898009962;T:3473768461;N:3510397 126 126     3508280857 4757668643 4898009962 3473768461 3510397 ERX11454466 ERS16387708 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.86106 0.86111 0.16002 0.16307 0.7653 0.76542 0.72623 0.70444 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14891 14891 ERR12071840 ERX11454465 ERS16387707 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E80 1 SAMEA114399015 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:80 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:80 1|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:296 66723 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 80-1_S37_L008_R1_001.fastq.gz 80-1_S37_L008_R2_001.fastq.gz fastq fastq 15269215248.0 60592124.0 ena RUN TAB 21 09 2023 13:32:15:296 66724 0:126 1:126 A:3161128702;C:4439474080;G:4571245477;T:3094451760;N:2915229 126 126     3161128702 4439474080 4571245477 3094451760 2915229 ERX11454465 ERS16387707 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.84008 0.83924 0.16203 0.16482 0.78486 0.78301 0.76847 0.76451 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14892 14892 ERR12071839 ERX11454464 ERS16387706 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E115 5 SAMEA114399014 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:115 5|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:115 5|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:296 66721 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 115-5_S28_L005_R2_001.fastq.gz 115-5_S28_L005_R1_001.fastq.gz fastq fastq 13704997824.0 54384912.0 ena RUN TAB 21 09 2023 13:32:15:296 66722 0:126 1:126 A:2791048995;C:4040751875;G:4161655954;T:2708992373;N:2548627 126 126     2791048995 4040751875 4161655954 2708992373 2548627 ERX11454464 ERS16387706 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.92152 0.922 0.16432 0.16746 0.77977 0.77723 0.7658 0.74319 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14893 14893 ERR12071838 ERX11454463 ERS16387705 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E115 4 SAMEA114399013 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:115 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:115 4|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:295 66719 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 115-4_S73_L007_R1_001.fastq.gz 115-4_S73_L007_R2_001.fastq.gz fastq fastq 13555374840.0 53791170.0 ena RUN TAB 21 09 2023 13:32:15:295 66720 0:126 1:126 A:2613879041;C:4131073531;G:4251239682;T:2536011431;N:23171155 126 126     2613879041 4131073531 4251239682 2536011431 23171155 ERX11454463 ERS16387705 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.93971 0.93992 0.15435 0.15669 0.78766 0.79076 0.76218 0.78676 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14894 14894 ERR12071837 ERX11454462 ERS16387704 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E115 2 SAMEA114399012 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:115 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:115 2|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:295 66717 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 115-2_S77_L008_R1_001.fastq.gz 115-2_S77_L008_R2_001.fastq.gz fastq fastq 19309168872.0 76623686.0 ena RUN TAB 21 09 2023 13:32:15:295 66718 0:126 1:126 A:3659403129;C:5914313547;G:6102556630;T:3596021103;N:36874463 126 126     3659403129 5914313547 6102556630 3596021103 36874463 ERX11454462 ERS16387704 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.90206 0.90085 0.164 0.16686 0.81477 0.81856 0.84674 0.83786 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14895 14895 ERR12071835 ERX11454460 ERS16387702 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E114 5 SAMEA114399010 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:114 5|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:114 5|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:294 66713 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 114-5_S68_L006_R1_001.fastq.gz 114-5_S68_L006_R2_001.fastq.gz fastq fastq 14161249872.0 56195436.0 ena RUN TAB 21 09 2023 13:32:15:295 66714 0:126 1:126 A:2927386834;C:4098238005;G:4213138034;T:2900333935;N:22153064 126 126     2927386834 4098238005 4213138034 2900333935 22153064 ERX11454460 ERS16387702 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.92035 0.91983 0.16785 0.17009 0.75864 0.76292 0.73081 0.75429 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14896 14896 ERR12071834 ERX11454459 ERS16387701 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E114 4 SAMEA114399009 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:114 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:114 4|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:294 66711 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 114-4_S76_L008_R1_001.fastq.gz 114-4_S76_L008_R2_001.fastq.gz fastq fastq 12939456600.0 51347050.0 ena RUN TAB 21 09 2023 13:32:15:294 66712 0:126 1:126 A:2686900916;C:3725092053;G:3826228928;T:2676529407;N:24705296 126 126     2686900916 3725092053 3826228928 2676529407 24705296 ERX11454459 ERS16387701 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.9171 0.91541 0.19718 0.20005 0.76759 0.77285 0.75547 0.75357 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14897 14897 ERR12071833 ERX11454458 ERS16387700 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E114 3 SAMEA114399008 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:114 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:114 3|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:294 66709 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 114-3_S72_L007_R1_001.fastq.gz 114-3_S72_L007_R2_001.fastq.gz fastq fastq 15510255012.0 61548631.0 ena RUN TAB 21 09 2023 13:32:15:294 66710 0:126 1:126 A:3024458012;C:4641826332;G:4764527525;T:3052903565;N:26539578 126 126     3024458012 4641826332 4764527525 3052903565 26539578 ERX11454458 ERS16387700 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.85112 0.84868 0.17054 0.17432 0.79547 0.79851 0.73756 0.8091 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14898 14898 ERR12071832 ERX11454457 ERS16387699 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E114 1 SAMEA114399007 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:114 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:114 1|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:294 66707 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 114-1_S27_L005_R1_001.fastq.gz 114-1_S27_L005_R2_001.fastq.gz fastq fastq 15544755576.0 61685538.0 ena RUN TAB 21 09 2023 13:32:15:294 66708 0:126 1:126 A:3077913021;C:4638218386;G:4760672592;T:3065112184;N:2839393 126 126     3077913021 4638218386 4760672592 3065112184 2839393 ERX11454457 ERS16387699 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.90822 0.90777 0.1775 0.18112 0.79263 0.78808 0.82214 0.79489 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14899 14899 ERR12071831 ERX11454456 ERS16387698 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E113 9 SAMEA114399006 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:113 9|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:113 9|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:293 66705 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 113-9_S67_L006_R1_001.fastq.gz 113-9_S67_L006_R2_001.fastq.gz fastq fastq 15414133644.0 61167197.0 ena RUN TAB 21 09 2023 13:32:15:293 66706 0:126 1:126 A:3185120611;C:4467167719;G:4606569127;T:3131094561;N:24181626 126 126     3185120611 4467167719 4606569127 3131094561 24181626 ERX11454456 ERS16387698 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.94176 0.94197 0.17489 0.17743 0.76063 0.76295 0.75218 0.75546 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14900 14900 ERR12071830 ERX11454455 ERS16387697 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E113 13 SAMEA114399005 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:113 13|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:113 13|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:293 66703 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 113-13_S71_L007_R1_001.fastq.gz 113-13_S71_L007_R2_001.fastq.gz fastq fastq 18125498160.0 71926580.0 ena RUN TAB 21 09 2023 13:32:15:293 66704 0:126 1:126 A:3681246224;C:5316613237;G:5486708206;T:3609735923;N:31194570 126 126     3681246224 5316613237 5486708206 3609735923 31194570 ERX11454455 ERS16387697 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.93952 0.93814 0.1717 0.17395 0.76627 0.76976 0.76533 0.72702 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14901 14901 ERR12071829 ERX11454454 ERS16387696 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E113 11 SAMEA114399004 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:113 11|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:113 11|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:293 66701 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 113-11_S26_L005_R1_001.fastq.gz 113-11_S26_L005_R2_001.fastq.gz fastq fastq 17918758872.0 71106186.0 ena RUN TAB 21 09 2023 13:32:15:293 66702 0:126 1:126 A:3460235614;C:5469489967;G:5622549540;T:3363214846;N:3268905 126 126     3460235614 5469489967 5622549540 3363214846 3268905 ERX11454454 ERS16387696 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.94836 0.94773 0.16512 0.16708 0.79843 0.79251 0.79716 0.79211 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14902 14902 ERR12071828 ERX11454453 ERS16387695 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E113 10 SAMEA114399003 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:113 10|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:113 10|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:293 66699 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 113-10_S75_L008_R1_001.fastq.gz 113-10_S75_L008_R2_001.fastq.gz fastq fastq 22137738588.0 87848169.0 ena RUN TAB 21 09 2023 13:32:15:293 66700 0:126 1:126 A:4240961737;C:6714114283;G:6924397580;T:4216314997;N:41949991 126 126     4240961737 6714114283 6924397580 4216314997 41949991 ERX11454453 ERS16387695 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.94101 0.93949 0.15969 0.16256 0.782 0.78429 0.78877 0.78359 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14903 14903 ERR12071827 ERX11454452 ERS16387694 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E112 8 SAMEA114399002 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:112 8|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:112 8|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:292 66697 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 112-8_S74_L008_R1_001.fastq.gz 112-8_S74_L008_R2_001.fastq.gz fastq fastq 15579825912.0 61824706.0 ena RUN TAB 21 09 2023 13:32:15:292 66698 0:126 1:126 A:3262384535;C:4470619467;G:4585527202;T:3231451715;N:29842993 126 126     3262384535 4470619467 4585527202 3231451715 29842993 ERX11454452 ERS16387694 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.92603 0.92484 0.18249 0.18589 0.75917 0.76335 0.73196 0.72728 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14904 14904 ERR12071826 ERX11454451 ERS16387693 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E112 7 SAMEA114399001 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:112 7|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:112 7|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:292 66695 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 112-7_S66_L006_R1_001.fastq.gz 112-7_S66_L006_R2_001.fastq.gz fastq fastq 20203529976.0 80172738.0 ena RUN TAB 21 09 2023 13:32:15:292 66696 0:126 1:126 A:4115948087;C:5902381830;G:6064166888;T:4089530757;N:31502414 126 126     4115948087 5902381830 6064166888 4089530757 31502414 ERX11454451 ERS16387693 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.92896 0.92845 0.17083 0.17434 0.76146 0.76337 0.6945 0.74323 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14905 14905 ERR12071825 ERX11454450 ERS16387692 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E112 5 SAMEA114399000 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:112 5|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:112 5|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:292 66693 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 112-5_S70_L007_R1_001.fastq.gz 112-5_S70_L007_R2_001.fastq.gz fastq fastq 14979433392.0 59442196.0 ena RUN TAB 21 09 2023 13:32:15:292 66694 0:126 1:126 A:2989976300;C:4427492967;G:4545641644;T:2990769657;N:25552824 126 126     2989976300 4427492967 4545641644 2990769657 25552824 ERX11454450 ERS16387692 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.9139 0.91293 0.18796 0.1912 0.78443 0.78597 0.79005 0.77582 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14906 14906 ERR12071824 ERX11454449 ERS16387691 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E112 4 SAMEA114398999 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:112 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:112 4|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:292 66691 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 112-4_S25_L005_R1_001.fastq.gz 112-4_S25_L005_R2_001.fastq.gz fastq fastq 14850028368.0 58928684.0 ena RUN TAB 21 09 2023 13:32:15:292 66692 0:126 1:126 A:3108605429;C:4289376091;G:4392727411;T:3056545411;N:2774026 126 126     3108605429 4289376091 4392727411 3056545411 2774026 ERX11454449 ERS16387691 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.92451 0.92555 0.17853 0.18265 0.76501 0.76106 0.73074 0.72504 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14907 14907 ERR12071823 ERX11454448 ERS16387690 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E111 4 SAMEA114398998 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:111 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:111 4|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:291 66689 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 111-4_S8_L002_R1_001.fastq.gz 111-4_S8_L002_R2_001.fastq.gz fastq fastq 17826911676.0 70741713.0 ena RUN TAB 21 09 2023 13:32:15:291 66690 0:126 1:126 A:3435687537;C:5460019012;G:5625529849;T:3303228205;N:2447073 126 126     3435687537 5460019012 5625529849 3303228205 2447073 ERX11454448 ERS16387690 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.95917 0.95936 0.18841 0.18992 0.81367 0.81523 0.79429 0.81623 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14908 14908 ERR12071822 ERX11454447 ERS16387689 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E111 3 SAMEA114398997 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:111 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:111 3|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:291 66687 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 111-3_S16_L004_R1_001.fastq.gz 111-3_S16_L004_R2_001.fastq.gz fastq fastq 16893915192.0 67039346.0 ena RUN TAB 21 09 2023 13:32:15:291 66688 0:126 1:126 A:3264486030;C:5167828698;G:5330646003;T:3128597235;N:2357226 126 126     3264486030 5167828698 5330646003 3128597235 2357226 ERX11454447 ERS16387689 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.96382 0.96339 0.19876 0.20112 0.81893 0.82102 0.81987 0.79966 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14909 14909 ERR12071821 ERX11454446 ERS16387688 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E111 2 SAMEA114398996 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:111 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:111 2|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:291 66685 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 111-2_S12_L003_R1_001.fastq.gz 111-2_S12_L003_R2_001.fastq.gz fastq fastq 19135485684.0 75934467.0 ena RUN TAB 21 09 2023 13:32:15:291 66686 0:126 1:126 A:3609533802;C:5946063742;G:6161038930;T:3416257009;N:2592201 126 126     3609533802 5946063742 6161038930 3416257009 2592201 ERX11454446 ERS16387688 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.96183 0.96186 0.17579 0.17791 0.81972 0.82047 0.77379 0.82377 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14910 14910 ERR12071820 ERX11454445 ERS16387687 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E111 1 SAMEA114398995 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:111 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:111 1|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:291 66683 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 111-1_S4_L001_R1_001.fastq.gz 111-1_S4_L001_R2_001.fastq.gz fastq fastq 21082514796.0 83660773.0 ena RUN TAB 21 09 2023 13:32:15:291 66684 0:126 1:126 A:4043020782;C:6480787651;G:6689150606;T:3865255761;N:4299996 126 126     4043020782 6480787651 6689150606 3865255761 4299996 ERX11454445 ERS16387687 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.96289 0.963 0.18676 0.18828 0.81791 0.81988 0.78774 0.81813 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14911 14911 ERR12071819 ERX11454444 ERS16387686 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E110 4 SAMEA114398994 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:110 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:110 4|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:290 66681 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 110-4_S3_L001_R2_001.fastq.gz 110-4_S3_L001_R1_001.fastq.gz fastq fastq 14687310204.0 58282977.0 ena RUN TAB 21 09 2023 13:32:15:290 66682 0:126 1:126 A:2926150199;C:4367282172;G:4510560380;T:2880182221;N:3135232 126 126     2926150199 4367282172 4510560380 2880182221 3135232 ERX11454444 ERS16387686 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.93442 0.934 0.1706 0.17527 0.77611 0.7782 0.79075 0.77981 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14912 14912 ERR12071818 ERX11454443 ERS16387685 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E110 3 SAMEA114398993 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:110 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:110 3|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:290 66679 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 110-3_S11_L003_R2_001.fastq.gz 110-3_S11_L003_R1_001.fastq.gz fastq fastq 13850712792.0 54963146.0 ena RUN TAB 21 09 2023 13:32:15:290 66680 0:126 1:126 A:2754372507;C:4139837776;G:4290528181;T:2664097645;N:1876683 126 126     2754372507 4139837776 4290528181 2664097645 1876683 ERX11454443 ERS16387685 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.94187 0.94169 0.16695 0.17006 0.77824 0.78044 0.7861 0.7945 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14913 14913 ERR12071817 ERX11454442 ERS16387684 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E110 2 SAMEA114398992 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:110 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:110 2|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:290 66677 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 110-2_S15_L004_R2_001.fastq.gz 110-2_S15_L004_R1_001.fastq.gz fastq fastq 15866607708.0 62962729.0 ena RUN TAB 21 09 2023 13:32:15:290 66678 0:126 1:126 A:3214891728;C:4688310800;G:4841314699;T:3119879854;N:2210627 126 126     3214891728 4688310800 4841314699 3119879854 2210627 ERX11454442 ERS16387684 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.93647 0.93604 0.16699 0.17 0.76641 0.76909 0.76728 0.77117 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14914 14914 ERR12071816 ERX11454441 ERS16387683 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E110 1 SAMEA114398991 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:110 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:110 1|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:290 66675 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 110-1_S7_L002_R2_001.fastq.gz 110-1_S7_L002_R1_001.fastq.gz fastq fastq 15365002212.0 60972231.0 ena RUN TAB 21 09 2023 13:32:15:290 66676 0:126 1:126 A:3114598527;C:4531528684;G:4684815069;T:3031977480;N:2082452 126 126     3114598527 4531528684 4684815069 3031977480 2082452 ERX11454441 ERS16387683 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.93661 0.936 0.17032 0.17368 0.7699 0.77157 0.74201 0.77289 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14915 14915 ERR12071815 ERX11454440 ERS16387682 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E109 4 SAMEA114398990 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:109 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:109 4|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:289 66673 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 109-4_S14_L004_R1_001.fastq.gz 109-4_S14_L004_R2_001.fastq.gz fastq fastq 17693786880.0 70213440.0 ena RUN TAB 21 09 2023 13:32:15:289 66674                       ERX11454440 ERS16387682 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.93895 0.93626 0.13454 0.13567 0.80679 0.80906 0.83187 0.85713 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14916 14916 ERR12071814 ERX11454439 ERS16387681 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E109 3 SAMEA114398989 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:109 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:109 3|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:289 66671 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 109-3_S6_L002_R1_001.fastq.gz 109-3_S6_L002_R2_001.fastq.gz fastq fastq 15326268300.0 60818525.0 ena RUN TAB 21 09 2023 13:32:15:289 66672 0:126 1:126 A:2963028716;C:4693248657;G:4853138006;T:2814772075;N:2080846 126 126     2963028716 4693248657 4853138006 2814772075 2080846 ERX11454439 ERS16387681 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.95492 0.95516 0.18592 0.18766 0.816 0.81722 0.82037 0.77416 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14917 14917 ERR12071813 ERX11454438 ERS16387680 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E109 2 SAMEA114398988 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:109 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:109 2|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:289 66669 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 109-2_S9_L003_R1_001.fastq.gz 109-2_S9_L003_R2_001.fastq.gz fastq fastq 13463300088.0 53425794.0 ena RUN TAB 21 09 2023 13:32:15:289 66670 0:126 1:126 A:2565791374;C:4152722401;G:4318203775;T:2424775489;N:1807049 126 126     2565791374 4152722401 4318203775 2424775489 1807049 ERX11454438 ERS16387680 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.96145 0.9621 0.19448 0.19497 0.83382 0.83451 0.84292 0.79683 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14918 14918 ERR12071812 ERX11454437 ERS16387679 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E109 1 SAMEA114398987 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:109 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:109 1|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:288 66667 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 109-1_S1_L001_R2_001.fastq.gz 109-1_S1_L001_R1_001.fastq.gz fastq fastq 16254330624.0 64501312.0 ena RUN TAB 21 09 2023 13:32:15:289 66668 0:126 1:126 A:3146898181;C:4962037311;G:5139473645;T:3002518241;N:3403246 126 126     3146898181 4962037311 5139473645 3002518241 3403246 ERX11454437 ERS16387679 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.95901 0.9593 0.19067 0.19204 0.8174 0.81864 0.7987 0.8132 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14919 14919 ERR12071811 ERX11454436 ERS16387678 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E108 4 SAMEA114398986 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:108 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:108 4|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:288 66665 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 108-4_S10_L003_R1_001.fastq.gz 108-4_S10_L003_R2_001.fastq.gz fastq fastq 16401717108.0 65086179.0 ena RUN TAB 21 09 2023 13:32:15:288 66666 0:126 1:126 A:3306091376;C:4834896468;G:4995683070;T:3262829888;N:2216306 126 126     3306091376 4834896468 4995683070 3262829888 2216306 ERX11454436 ERS16387678 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.92612 0.92543 0.16352 0.16724 0.76607 0.76812 0.76693 0.75698 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14920 14920 ERR12071810 ERX11454435 ERS16387677 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E108 3 SAMEA114398985 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:108 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:108 3|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:288 66663 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 108-3_S2_L001_R2_001.fastq.gz 108-3_S2_L001_R1_001.fastq.gz fastq fastq 14063114268.0 55806009.0 ena RUN TAB 21 09 2023 13:32:15:288 66664 0:126 1:126 A:2855140106;C:4126986255;G:4254731693;T:2823386830;N:2869384 126 126     2855140106 4126986255 4254731693 2823386830 2869384 ERX11454435 ERS16387677 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.89956 0.89846 0.17394 0.17665 0.77695 0.77751 0.78333 0.77908 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14921 14921 ERR12071809 ERX11454434 ERS16387676 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E108 2 SAMEA114398984 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:108 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:108 2|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:288 66661 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 108-2_S13_L004_R1_001.fastq.gz 108-2_S13_L004_R2_001.fastq.gz fastq fastq 17951370444.0 71235597.0 ena RUN TAB 21 09 2023 13:32:15:288 66662 0:126 1:126 A:3419406758;C:5496702371;G:5719743964;T:3312990750;N:2526601 126 126     3419406758 5496702371 5719743964 3312990750 2526601 ERX11454434 ERS16387676 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.91308 0.91164 0.14161 0.14408 0.78725 0.78851 0.77166 0.81536 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14922 14922 ERR12071808 ERX11454433 ERS16387675 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E108 1 SAMEA114398983 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:108 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:108 1|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:287 66659 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 108-1_S5_L002_R1_001.fastq.gz 108-1_S5_L002_R2_001.fastq.gz fastq fastq 17592295140.0 69810695.0 ena RUN TAB 21 09 2023 13:32:15:288 66660 0:126 1:126 A:3473054128;C:5265562453;G:5455395791;T:3395881406;N:2401362 126 126     3473054128 5265562453 5455395791 3395881406 2401362 ERX11454433 ERS16387675 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.92632 0.92464 0.16285 0.16525 0.7781 0.77985 0.79539 0.79841 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14923 14923 ERR12071807 ERX11454432 ERS16387674 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E107 4 SAMEA114398982 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:107 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:107 4|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:287 66657 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 107-4_S20_L005_R1_001.fastq.gz 107-4_S20_L005_R2_001.fastq.gz fastq fastq 12626647992.0 50105746.0 ena RUN TAB 21 09 2023 13:32:15:287 66658 0:126 1:126 A:2503116695;C:3776878144;G:3904732537;T:2438634661;N:3285955 126 126     2503116695 3776878144 3904732537 2438634661 3285955 ERX11454432 ERS16387674 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.93409 0.93399 0.16467 0.16803 0.77567 0.77749 0.77962 0.76236 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14924 14924 ERR12071806 ERX11454431 ERS16387673 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E107 3 SAMEA114398981 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:107 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:107 3|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:287 66655 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 107-3_S28_L007_R1_001.fastq.gz 107-3_S28_L007_R2_001.fastq.gz fastq fastq 19765610928.0 78434964.0 ena RUN TAB 21 09 2023 13:32:15:287 66656 0:126 1:126 A:3807913538;C:6041902918;G:6270499946;T:3639644996;N:5649530 126 126     3807913538 6041902918 6270499946 3639644996 5649530 ERX11454431 ERS16387673 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.93479 0.93431 0.15154 0.15299 0.78462 0.78533 0.78429 0.79385 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14925 14925 ERR12071805 ERX11454430 ERS16387672 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E107 2 SAMEA114398980 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:107 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:107 2|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:287 66653 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 107-2_S32_L008_R1_001.fastq.gz 107-2_S32_L008_R2_001.fastq.gz fastq fastq 20245786344.0 80340422.0 ena RUN TAB 21 09 2023 13:32:15:287 66654 0:126 1:126 A:3580212812;C:6483019868;G:6732117106;T:3443314781;N:7121777 126 126     3580212812 6483019868 6732117106 3443314781 7121777 ERX11454430 ERS16387672 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.93526 0.93431 0.14042 0.14264 0.82887 0.83041 0.85552 0.85524 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14926 14926 ERR12071804 ERX11454429 ERS16387671 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E107 1 SAMEA114398979 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:107 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:107 1|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:286 66651 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 107-1_S24_L006_R2_001.fastq.gz 107-1_S24_L006_R1_001.fastq.gz fastq fastq 15192276120.0 60286810.0 ena RUN TAB 21 09 2023 13:32:15:286 66652 0:126 1:126 A:2840014487;C:4709824279;G:4867364305;T:2771588673;N:3484376 126 126     2840014487 4709824279 4867364305 2771588673 3484376 ERX11454429 ERS16387671 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.92039 0.91914 0.17007 0.17237 0.80939 0.80986 0.84885 0.847 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14927 14927 ERR12071803 ERX11454428 ERS16387670 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E106 4 SAMEA114398978 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:106 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:106 4|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:286 66649 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 106-4_S23_L006_R2_001.fastq.gz 106-4_S23_L006_R1_001.fastq.gz fastq fastq 16985562300.0 67403025.0 ena RUN TAB 21 09 2023 13:32:15:286 66650 0:126 1:126 A:3322275260;C:5133904780;G:5334495158;T:3190965461;N:3921641 126 126     3322275260 5133904780 5334495158 3190965461 3921641 ERX11454428 ERS16387670 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.93707 0.93661 0.15576 0.15861 0.77826 0.78025 0.77722 0.77979 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14928 14928 ERR12071802 ERX11454427 ERS16387669 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E106 3 SAMEA114398977 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:106 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:106 3|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:286 66647 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 106-3_S31_L008_R2_001.fastq.gz 106-3_S31_L008_R1_001.fastq.gz fastq fastq 19459285524.0 77219387.0 ena RUN TAB 21 09 2023 13:32:15:286 66648 0:126 1:126 A:3823996295;C:5872737349;G:6122836793;T:3632881865;N:6833222 126 126     3823996295 5872737349 6122836793 3632881865 6833222 ERX11454427 ERS16387669 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.90902 0.90816 0.1544 0.15713 0.78926 0.79176 0.76867 0.78913 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14929 14929 ERR12071801 ERX11454426 ERS16387668 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E106 2 SAMEA114398976 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:106 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:106 2|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:285 66645 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 106-2_S27_L007_R1_001.fastq.gz 106-2_S27_L007_R2_001.fastq.gz fastq fastq 15694418124.0 62279437.0 ena RUN TAB 21 09 2023 13:32:15:286 66646 0:126 1:126 A:3002717019;C:4829058190;G:5037608362;T:2820533482;N:4501071 126 126     3002717019 4829058190 5037608362 2820533482 4501071 ERX11454426 ERS16387668 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.93511 0.93528 0.14004 0.14226 0.7891 0.79068 0.77063 0.77891 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14930 14930 ERR12071800 ERX11454425 ERS16387667 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E106 1 SAMEA114398975 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:106 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:106 1|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:285 66643 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 106-1_S19_L005_R1_001.fastq.gz 106-1_S19_L005_R2_001.fastq.gz fastq fastq 18647636868.0 73998559.0 ena RUN TAB 21 09 2023 13:32:15:285 66644 0:126 1:126 A:3692341453;C:5587227660;G:5803402834;T:3559657331;N:5007590 126 126     3692341453 5587227660 5803402834 3559657331 5007590 ERX11454425 ERS16387667 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.92714 0.92688 0.16214 0.16642 0.77433 0.775 0.76217 0.75322 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14931 14931 ERR12071799 ERX11454424 ERS16387666 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E105 4 SAMEA114398974 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:105 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:105 4|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:285 66641 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 105-4_S26_L007_R2_001.fastq.gz 105-4_S26_L007_R1_001.fastq.gz fastq fastq 15124522392.0 60017946.0 ena RUN TAB 21 09 2023 13:32:15:285 66642 0:126 1:126 A:2852895871;C:4689063320;G:4867825391;T:2710443233;N:4294577 126 126     2852895871 4689063320 4867825391 2710443233 4294577 ERX11454424 ERS16387666 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.95529 0.95479 0.13148 0.13281 0.7793 0.78125 0.78337 0.78508 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14932 14932 ERR12071798 ERX11454423 ERS16387665 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E105 3 SAMEA114398973 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:105 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:105 3|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:285 66639 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 105-3_S18_L005_R1_001.fastq.gz 105-3_S18_L005_R2_001.fastq.gz fastq fastq 17644367664.0 70017332.0 ena RUN TAB 21 09 2023 13:32:15:285 66640 0:126 1:126 A:3347478814;C:5457952160;G:5642901286;T:3191260656;N:4774748 126 126     3347478814 5457952160 5642901286 3191260656 4774748 ERX11454423 ERS16387665 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.94866 0.94893 0.14303 0.14517 0.78658 0.78697 0.80916 0.81131 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14933 14933 ERR12071797 ERX11454422 ERS16387664 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E105 2 SAMEA114398972 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:105 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:105 2|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:284 66637 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 105-2_S30_L008_R1_001.fastq.gz 105-2_S30_L008_R2_001.fastq.gz fastq fastq 15981084252.0 63417001.0 ena RUN TAB 21 09 2023 13:32:15:285 66638 0:126 1:126 A:3059876138;C:4898463877;G:5076925794;T:2940239108;N:5579335 126 126     3059876138 4898463877 5076925794 2940239108 5579335 ERX11454422 ERS16387664 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.95109 0.95022 0.14624 0.14776 0.78066 0.78283 0.76738 0.79238 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14934 14934 ERR12071796 ERX11454421 ERS16387663 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E105 1 SAMEA114398971 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:105 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:105 1|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:284 66635 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 105-1_S22_L006_R1_001.fastq.gz 105-1_S22_L006_R2_001.fastq.gz fastq fastq 16378597368.0 64994434.0 ena RUN TAB 21 09 2023 13:32:15:284 66636 0:126 1:126 A:3157768088;C:4992606167;G:5190605482;T:3033853059;N:3764572 126 126     3157768088 4992606167 5190605482 3033853059 3764572 ERX11454421 ERS16387663 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.9472 0.94619 0.15768 0.15997 0.78646 0.78845 0.75864 0.79159 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14935 14935 ERR12071795 ERX11454420 ERS16387662 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E104 4 SAMEA114398970 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:104 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:104 4|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:284 66633 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 104-4_S29_L008_R2_001.fastq.gz 104-4_S29_L008_R1_001.fastq.gz fastq fastq 17713234476.0 70290613.0 ena RUN TAB 21 09 2023 13:32:15:284 66634 0:126 1:126 A:3387663411;C:5419734351;G:5646953646;T:3252634316;N:6248752 126 126     3387663411 5419734351 5646953646 3252634316 6248752 ERX11454420 ERS16387662 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.91957 0.91797 0.14938 0.15201 0.79149 0.79358 0.7508 0.80456 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14936 14936 ERR12071794 ERX11454419 ERS16387661 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E104 3 SAMEA114398969 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:104 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:104 3|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:284 66631 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 104-3_S21_L006_R1_001.fastq.gz 104-3_S21_L006_R2_001.fastq.gz fastq fastq 20412904428.0 81003589.0 ena RUN TAB 21 09 2023 13:32:15:284 66632 0:126 1:126 A:3999139733;C:6180998229;G:6441889554;T:3786215014;N:4661898 126 126     3999139733 6180998229 6441889554 3786215014 4661898 ERX11454419 ERS16387661 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.93627 0.93494 0.14845 0.14979 0.77796 0.77891 0.76434 0.77202 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14937 14937 ERR12071793 ERX11454418 ERS16387660 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E104 2 SAMEA114398968 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:104 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:104 2|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:283 66629 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 104-2_S25_L007_R1_001.fastq.gz 104-2_S25_L007_R2_001.fastq.gz fastq fastq 15067973340.0 59793545.0 ena RUN TAB 21 09 2023 13:32:15:284 66630 0:126 1:126 A:2963040605;C:4540311477;G:4736958045;T:2823360579;N:4302634 126 126     2963040605 4540311477 4736958045 2823360579 4302634 ERX11454418 ERS16387660 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.92968 0.92854 0.16053 0.16248 0.78224 0.78228 0.7365 0.76845 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14938 14938 ERR12071792 ERX11454417 ERS16387659 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E104 1 SAMEA114398967 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:104 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:104 1|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:283 66627 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 104-1_S17_L005_R1_001.fastq.gz 104-1_S17_L005_R2_001.fastq.gz fastq fastq 19257494508.0 76418629.0 ena RUN TAB 21 09 2023 13:32:15:283 66628 0:126 1:126 A:3731156408;C:5859411051;G:6100994986;T:3560909583;N:5022480 126 126     3731156408 5859411051 6100994986 3560909583 5022480 ERX11454417 ERS16387659 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.92633 0.92586 0.14768 0.14948 0.78277 0.7833 0.7452 0.76737 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14939 14939 ERR12071791 ERX11454416 ERS16387658 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E103 4 SAMEA114398966 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:103 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:103 4|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:283 66625 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 103-4_S32_L006_R1_001.fastq.gz 103-4_S32_L006_R2_001.fastq.gz fastq fastq 13085486820.0 51926535.0 ena RUN TAB 21 09 2023 13:32:15:283 66626 0:126 1:126 A:2567103783;C:3969617611;G:4069486176;T:2476759371;N:2519879 126 126     2567103783 3969617611 4069486176 2476759371 2519879 ERX11454416 ERS16387658 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.93075 0.93242 0.14151 0.14331 0.774 0.76822 0.75401 0.76454 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14940 14940 ERR12071790 ERX11454415 ERS16387657 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E103 3 SAMEA114398965 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:103 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:103 3|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:283 66623 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 103-3_S65_L007_R2_001.fastq.gz 103-3_S65_L007_R1_001.fastq.gz fastq fastq 11192352696.0 44414098.0 ena RUN TAB 21 09 2023 13:32:15:283 66624 0:126 1:126 A:2123359510;C:3455439467;G:3570545494;T:2039990322;N:3017903 126 126     2123359510 3455439467 3570545494 2039990322 3017903 ERX11454415 ERS16387657 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.89542 0.89591 0.1351 0.13661 0.78948 0.79003 0.77414 0.80393 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14941 14941 ERR12071789 ERX11454414 ERS16387656 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E103 2 SAMEA114398964 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:103 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:103 2|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:282 66621 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 103-2_S36_L007_R1_001.fastq.gz 103-2_S36_L007_R2_001.fastq.gz fastq fastq 10568377512.0 41938006.0 ena RUN TAB 21 09 2023 13:32:15:283 66622 0:126 1:126 A:2109516452;C:3179785410;G:3272667938;T:2004453838;N:1953874 126 126     2109516452 3179785410 3272667938 2004453838 1953874 ERX11454414 ERS16387656 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.92729 0.92817 0.15094 0.1528 0.7685 0.76516 0.74143 0.74277 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14942 14942 ERR12071788 ERX11454413 ERS16387655 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E103 1 SAMEA114398963 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:103 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:103 1|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:282 66619 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 103-1_S69_L008_R1_001.fastq.gz 103-1_S69_L008_R2_001.fastq.gz fastq fastq 9417798180.0 37372215.0 ena RUN TAB 21 09 2023 13:32:15:282 66620 0:126 1:126 A:1807793384;C:2891759578;G:2983948236;T:1730405095;N:3891887 126 126     1807793384 2891759578 2983948236 1730405095 3891887 ERX11454413 ERS16387655 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.8784 0.87802 0.13342 0.13445 0.789 0.78946 0.79547 0.79885 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14943 14943 ERR12071787 ERX11454412 ERS16387654 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E102 4 SAMEA114398962 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:102 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:102 4|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:282 66617 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 102-4_S35_L007_R2_001.fastq.gz 102-4_S35_L007_R1_001.fastq.gz fastq fastq 15605254728.0 61925614.0 ena RUN TAB 21 09 2023 13:32:15:282 66618 0:126 1:126 A:3158918177;C:4616749707;G:4726409583;T:3100328707;N:2848554 126 126     3158918177 4616749707 4726409583 3100328707 2848554 ERX11454412 ERS16387654 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.91674 0.91732 0.1668 0.16991 0.77569 0.77082 0.76006 0.76056 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14944 14944 ERR12071786 ERX11454411 ERS16387653 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E102 3 SAMEA114398961 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:102 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:102 3|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:282 66615 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 102-3_S68_L008_R1_001.fastq.gz 102-3_S68_L008_R2_001.fastq.gz fastq fastq 20642076252.0 81913001.0 ena RUN TAB 21 09 2023 13:32:15:282 66616 0:126 1:126 A:3670199430;C:6557337612;G:6776033266;T:3629933781;N:8572163 126 126     3670199430 6557337612 6776033266 3629933781 8572163 ERX11454411 ERS16387653 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.89984 0.89794 0.14393 0.14603 0.82079 0.82233 0.83939 0.8347 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14945 14945 ERR12071785 ERX11454410 ERS16387652 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E102 2 SAMEA114398960 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:102 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:102 2|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:281 66613 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 22 102-2_S31_L006_R1_001.fastq.gz 102-2_S31_L006_R2_001.fastq.gz fastq fastq 23877621936.0 94752468.0 ena RUN TAB 21 09 2023 13:32:15:282 66614 0:126 1:126 A:3953279642;C:7876070920;G:8128759951;T:3914909602;N:4601821 126 126     3953279642 7876070920 8128759951 3914909602 4601821 ERX11454410 ERS16387652 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.92602 0.85538 0.13016 0.12286 0.84508 0.84936 0.81613 0.88529 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14946 14946 ERR12071784 ERX11454409 ERS16387651 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   Low stress E102 1 SAMEA114398959 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:102 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:102 1|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:281 66611 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 102-1_S64_L007_R1_001.fastq.gz 102-1_S64_L007_R2_001.fastq.gz fastq fastq 20588587236.0 81700743.0 ena RUN TAB 21 09 2023 13:32:15:281 66612 0:126 1:126 A:3005365881;C:7167599347;G:7450281822;T:2959758690;N:5581496 126 126     3005365881 7167599347 7450281822 2959758690 5581496 ERX11454409 ERS16387651 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.90225 0.89979 0.08909 0.09003 0.87071 0.87148 0.90162 0.83246 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14947 14947 ERR12071783 ERX11454408 ERS16387650 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E101 4 SAMEA114398958 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:101 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:101 4|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:281 66609 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 101-4_S30_L006_R1_001.fastq.gz 101-4_S30_L006_R2_001.fastq.gz fastq fastq 12524862168.0 49701834.0 ena RUN TAB 21 09 2023 13:32:15:281 66610 0:126 1:126 A:2576891018;C:3688938717;G:3819872503;T:2436717421;N:2442509 126 126     2576891018 3688938717 3819872503 2436717421 2442509 ERX11454408 ERS16387650 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.92878 0.92997 0.15322 0.15505 0.76315 0.76063 0.69783 0.67569 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14948 14948 ERR12071782 ERX11454407 ERS16387649 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E101 3 SAMEA114398957 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:101 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:101 3|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:281 66607 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 101-3_S34_L007_R1_001.fastq.gz 101-3_S34_L007_R2_001.fastq.gz fastq fastq 11973395700.0 47513475.0 ena RUN TAB 21 09 2023 13:32:15:281 66608 0:126 1:126 A:2371769443;C:3605917515;G:3700919970;T:2292577579;N:2211193 126 126     2371769443 3605917515 3700919970 2292577579 2211193 ERX11454407 ERS16387649 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.92217 0.92315 0.14568 0.1469 0.7724 0.76917 0.7521 0.75171 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise
14949 14949 ERR12071781 ERX11454406 ERS16387648 ERP151293 PRJEB66218 Social stress in Zebrafish sperm b81525de-0f4f-4e41-8e34-f411e5590e7b Other Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21   High stress E101 2 SAMEA114398956 University of East Anglia INSDC center name:University of East Anglia|Submitter Id:101 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:101 2|scientific name:Danio rerio                 Illumina HiSeq X paired end sequencing ena EXPERIMENT TAB 21 09 2023 13:32:15:280 66605 125bp 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq X   ERP151293 Illumina HiSeq X paired end sequencing ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 101-2_S63_L007_R2_001.fastq.gz 101-2_S63_L007_R1_001.fastq.gz fastq fastq 10806069456.0 42881228.0 ena RUN TAB 21 09 2023 13:32:15:280 66606 0:126 1:126 A:2073944191;C:3321784426;G:3405352767;T:2002070301;N:2917771 126 126     2073944191 3321784426 3405352767 2002070301 2917771 ERX11454406 ERS16387648 ERA27252154 university of east anglia|European Nucleotide Archive university of east anglia 2 0.9236 0.92427 0.14372 0.14539 0.78084 0.78141 0.74294 0.78886 126 126 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2023-09-21 Undetermined Embryo Undetermined Embryo Imprecise

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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");;