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run_metadata

6,136 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "cDNA" and tissue_curation_coarse = "All anatomical structures"

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devstage_curation >10

technology 8

experiment.platform 7

devstage_curation_coarse 5

experiment.library_strategy 3

tissue_curation 2

experiment.library_source 2

tissue_curation_coarse 1

  • All anatomical structures · 6,136 ✖

experiment.library_selection 1

  • cDNA · 6,136 ✖

experiment.library_layout 1

  • SINGLE · 6,136 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
3015 3015 ERR1396841 ERX1468100 ERS1051448 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 C7 SAMEA3864314 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864314|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:35Z|INSDC status:public|Submitter Id:2a85d100 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a85d100 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#24 15616955 Illumina sequencing of library 15616955 constructed from sample accession ERS1051448 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence ATTCCT. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#24.cram cram 252742350.0 5054847.0 SC RUN 18732 2#24 0:50 A:72444190;C:64568625;G:62796637;T:52911792;N:21106 50       72444190 64568625 62796637 52911792 21106 ERX1468100 ERS1051448 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.61824   0.09608   0.8842   0.56978   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Embryo Imprecise All anatomical structures
3016 3016 ERR1396840 ERX1468099 ERS1051447 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 B12 SAMEA3864313 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864313|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:35Z|INSDC status:public|Submitter Id:2a7dbab0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a7dbab0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#23 15616943 Illumina sequencing of library 15616943 constructed from sample accession ERS1051447 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence ACTGAT. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#23.cram cram 911394150.0 18227883.0 SC RUN 18732 2#23 0:50 A:264591252;C:227216187;G:236072241;T:183438530;N:75940 50       264591252 227216187 236072241 183438530 75940 ERX1468099 ERS1051447 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.58273   0.09754   0.87448   0.55833   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3017 3017 ERR1396839 ERX1468098 ERS1051446 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 B10 SAMEA3864312 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864312|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:34Z|INSDC status:public|Submitter Id:2a70e970 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a70e970 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#22 15616931 Illumina sequencing of library 15616931 constructed from sample accession ERS1051446 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GAGTGG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#22.cram cram 242466400.0 4849328.0 SC RUN 18732 2#22 0:50 A:69326734;C:60104801;G:65507097;T:47507301;N:20467 50       69326734 60104801 65507097 47507301 20467 ERX1468098 ERS1051446 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.60819   0.09544   0.87864   0.58472   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3018 3018 ERR1396838 ERX1468097 ERS1051445 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 B3 SAMEA3864311 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864311|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:34Z|INSDC status:public|Submitter Id:2a6aa7e0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a6aa7e0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#21 15616919 Illumina sequencing of library 15616919 constructed from sample accession ERS1051445 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence CGTACG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#21.cram cram 630737800.0 12614756.0 SC RUN 18732 2#21 0:50 A:180007611;C:161281943;G:164376347;T:125019243;N:52656 50       180007611 161281943 164376347 125019243 52656 ERX1468097 ERS1051445 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.62407   0.10189   0.87825   0.57526   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3019 3019 ERR1396837 ERX1468096 ERS1051444 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 A4 SAMEA3864310 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864310|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:33Z|INSDC status:public|Submitter Id:2a61a730 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a61a730 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#20 15616907 Illumina sequencing of library 15616907 constructed from sample accession ERS1051444 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GTTTCG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#20.cram cram 488336450.0 9766729.0 SC RUN 18732 2#20 0:50 A:137910201;C:123586221;G:128373512;T:98425645;N:40871 50       137910201 123586221 128373512 98425645 40871 ERX1468096 ERS1051444 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.5453   0.11361   0.86594   0.58106   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3020 3020 ERR1396836 ERX1468095 ERS1051443 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 A3 SAMEA3864309 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864309|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:32Z|INSDC status:public|Submitter Id:2a5a0610 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a5a0610 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#19 15616895 Illumina sequencing of library 15616895 constructed from sample accession ERS1051443 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GTGGCC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#19.cram cram 502748050.0 10054961.0 SC RUN 18732 2#19 0:50 A:140684190;C:129525504;G:133998850;T:98497819;N:41687 50       140684190 129525504 133998850 98497819 41687 ERX1468095 ERS1051443 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.55085   0.11739   0.87077   0.6012   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3021 3021 ERR1396835 ERX1468094 ERS1051442 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 A2 SAMEA3864308 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864308|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:32Z|INSDC status:public|Submitter Id:2a537660 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a537660 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#18 15616883 Illumina sequencing of library 15616883 constructed from sample accession ERS1051442 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GTGAAA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#18.cram cram 512343000.0 10246860.0 SC RUN 18732 2#18 0:50 A:149660992;C:130013834;G:134888430;T:97736324;N:43420 50       149660992 130013834 134888430 97736324 43420 ERX1468094 ERS1051442 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.54809   0.11505   0.88254   0.5985   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3022 3022 ERR1396834 ERX1468093 ERS1051441 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 A1 SAMEA3864307 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864307|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:31Z|INSDC status:public|Submitter Id:2a4c4a70 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a4c4a70 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#17 15616871 Illumina sequencing of library 15616871 constructed from sample accession ERS1051441 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GTCCGC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#17.cram cram 296362850.0 5927257.0 SC RUN 18732 2#17 0:50 A:84251830;C:79653531;G:76748992;T:55683722;N:24775 50       84251830 79653531 76748992 55683722 24775 ERX1468093 ERS1051441 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.50115   0.10395   0.90185   0.6019   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3023 3023 ERR1396833 ERX1468092 ERS1051440 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer C3 SAMEA3864306 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864306|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:31Z|INSDC status:public|Submitter Id:2a3ba8a0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a3ba8a0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#16 15616954 Illumina sequencing of library 15616954 constructed from sample accession ERS1051440 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence CCGTCC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#16.cram cram 247427250.0 4948545.0 SC RUN 18732 2#16 0:50 A:69477894;C:64165990;G:64753499;T:49009156;N:20711 50       69477894 64165990 64753499 49009156 20711 ERX1468092 ERS1051440 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.66601   0.10439   0.88156   0.5519   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3024 3024 ERR1396832 ERX1468091 ERS1051439 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer B4 SAMEA3864305 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864305|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:30Z|INSDC status:public|Submitter Id:2a319680 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a319680 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#15 15616942 Illumina sequencing of library 15616942 constructed from sample accession ERS1051439 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence ATGTCA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#15.cram cram 268495550.0 5369911.0 SC RUN 18732 2#15 0:50 A:78316008;C:67311837;G:69086954;T:53758238;N:22513 50       78316008 67311837 69086954 53758238 22513 ERX1468091 ERS1051439 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.61927   0.0935   0.89745   0.55698   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3025 3025 ERR1396831 ERX1468090 ERS1051438 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer A7 SAMEA3864304 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864304|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:29Z|INSDC status:public|Submitter Id:2a2a6a90 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a2a6a90 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#14 15616930 Illumina sequencing of library 15616930 constructed from sample accession ERS1051438 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence AGTTCC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#14.cram cram 457637200.0 9152744.0 SC RUN 18732 2#14 0:50 A:131304805;C:115755054;G:118778813;T:91760838;N:37690 50       131304805 115755054 118778813 91760838 37690 ERX1468090 ERS1051438 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.64717   0.09607   0.89832   0.56732   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3026 3026 ERR1396830 ERX1468089 ERS1051437 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer A1 SAMEA3864303 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864303|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:29Z|INSDC status:public|Submitter Id:2a238cc0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a238cc0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#13 15616918 Illumina sequencing of library 15616918 constructed from sample accession ERS1051437 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence AGTCAA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#13.cram cram 156613950.0 3132279.0 SC RUN 18732 2#13 0:50 A:45659102;C:39445557;G:40495414;T:31000827;N:13050 50       45659102 39445557 40495414 31000827 13050 ERX1468089 ERS1051437 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.65923   0.09289   0.90096   0.52171   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3027 3027 ERR1396829 ERX1468088 ERS1051436 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer C1 SAMEA3864302 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864302|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:28Z|INSDC status:public|Submitter Id:2a1b9d80 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a1b9d80 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#12 15616906 Illumina sequencing of library 15616906 constructed from sample accession ERS1051436 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence CTTGTA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#12.cram cram 370496150.0 7409923.0 SC RUN 18732 2#12 0:50 A:104657486;C:92274677;G:97465315;T:76068240;N:30432 50       104657486 92274677 97465315 76068240 30432 ERX1468088 ERS1051436 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.64244   0.11811   0.86578   0.55798   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3028 3028 ERR1396828 ERX1468087 ERS1051435 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer B3 SAMEA3864301 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864301|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:55Z|INSDC last update:2016 02 03T09:48:28Z|INSDC status:public|Submitter Id:2a0d93c0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a0d93c0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#11 15616894 Illumina sequencing of library 15616894 constructed from sample accession ERS1051435 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GGCTAC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#11.cram cram 136326100.0 2726522.0 SC RUN 18732 2#11 0:50 A:38914874;C:34737645;G:36229387;T:26432631;N:11563 50       38914874 34737645 36229387 26432631 11563 ERX1468087 ERS1051435 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.60295   0.10315   0.89092   0.58169   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3029 3029 ERR1396827 ERX1468086 ERS1051434 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer A12 SAMEA3864300 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864300|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:27Z|INSDC status:public|Submitter Id:2a075230 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a075230 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#10 15616882 Illumina sequencing of library 15616882 constructed from sample accession ERS1051434 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence TAGCTT. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#10.cram cram 257740250.0 5154805.0 SC RUN 18732 2#10 0:50 A:73736881;C:64681440;G:67096497;T:52203988;N:21444 50       73736881 64681440 67096497 52203988 21444 ERX1468086 ERS1051434 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.62041   0.10196   0.89706   0.55474   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3030 3030 ERR1396826 ERX1468085 ERS1051433 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer A10 SAMEA3864299 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864299|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:26Z|INSDC status:public|Submitter Id:29ffff30 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29ffff30 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#9 15616870 Illumina sequencing of library 15616870 constructed from sample accession ERS1051433 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GATCAG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#9.cram cram 7356000.0 147120.0 SC RUN 18732 2#9 0:50 A:2152284;C:1844982;G:1920243;T:1437897;N:594 50       2152284 1844982 1920243 1437897 594 ERX1468085 ERS1051433 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.60239   0.10502   0.91084   0.55869   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3031 3031 ERR1396825 ERX1468084 ERS1051432 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha C1 SAMEA3864298 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864298|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:26Z|INSDC status:public|Submitter Id:29f306e0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29f306e0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#8 15616953 Illumina sequencing of library 15616953 constructed from sample accession ERS1051432 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence ACTTGA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#8.cram cram 454519900.0 9090398.0 SC RUN 18732 2#8 0:50 A:133717355;C:117574792;G:114940340;T:88249706;N:37707 50       133717355 117574792 114940340 88249706 37707 ERX1468084 ERS1051432 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.51063   0.10053   0.88572   0.60434   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3032 3032 ERR1396824 ERX1468083 ERS1051431 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha A9 SAMEA3864297 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864297|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:25Z|INSDC status:public|Submitter Id:29e942e0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29e942e0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#7 15616941 Illumina sequencing of library 15616941 constructed from sample accession ERS1051431 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence CAGATC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#7.cram cram 288165650.0 5763313.0 SC RUN 18732 2#7 0:50 A:83874531;C:74578491;G:74739497;T:54949008;N:24123 50       83874531 74578491 74739497 54949008 24123 ERX1468083 ERS1051431 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.56561   0.10234   0.88278   0.59066   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3033 3033 ERR1396823 ERX1468082 ERS1051430 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha A6 SAMEA3864296 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864296|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:25Z|INSDC status:public|Submitter Id:29e06940 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29e06940 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#6 15616929 Illumina sequencing of library 15616929 constructed from sample accession ERS1051430 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GCCAAT. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#6.cram cram 234507600.0 4690152.0 SC RUN 18732 2#6 0:50 A:67284766;C:59565829;G:61407599;T:46229970;N:19436 50       67284766 59565829 61407599 46229970 19436 ERX1468082 ERS1051430 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.64334   0.10252   0.88905   0.5695   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3034 3034 ERR1396822 ERX1468081 ERS1051429 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha A1 SAMEA3864295 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864295|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:24Z|INSDC status:public|Submitter Id:29d74180 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29d74180 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#5 15616917 Illumina sequencing of library 15616917 constructed from sample accession ERS1051429 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence ACAGTG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#5.cram cram 161797350.0 3235947.0 SC RUN 18732 2#5 0:50 A:46711991;C:40739475;G:42456048;T:31876390;N:13446 50       46711991 40739475 42456048 31876390 13446 ERX1468081 ERS1051429 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.64666   0.09851   0.90508   0.56607   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3035 3035 ERR1396821 ERX1468080 ERS1051428 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha B12 SAMEA3864294 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864294|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:23Z|INSDC status:public|Submitter Id:29cf7950 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29cf7950 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#4 15616905 Illumina sequencing of library 15616905 constructed from sample accession ERS1051428 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence TGACCA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#4.cram cram 393377600.0 7867552.0 SC RUN 18732 2#4 0:50 A:115292812;C:103803007;G:98535312;T:75713409;N:33060 50       115292812 103803007 98535312 75713409 33060 ERX1468080 ERS1051428 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.51888   0.1037   0.89948   0.59445   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3036 3036 ERR1396820 ERX1468079 ERS1051427 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha B10 SAMEA3864293 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864293|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:22Z|INSDC status:public|Submitter Id:29c84d60 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29c84d60 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#3 15616893 Illumina sequencing of library 15616893 constructed from sample accession ERS1051427 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence TTAGGC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#3.cram cram 211138300.0 4222766.0 SC RUN 18732 2#3 0:50 A:60487130;C:53019786;G:55472125;T:42141858;N:17401 50       60487130 53019786 55472125 42141858 17401 ERX1468079 ERS1051427 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.57434   0.11571   0.88633   0.6058   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3037 3037 ERR1396819 ERX1468078 ERS1051426 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha B7 SAMEA3864292 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864292|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:22Z|INSDC status:public|Submitter Id:29b1df30 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29b1df30 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#2 15616881 Illumina sequencing of library 15616881 constructed from sample accession ERS1051426 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence CGATGT. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#2.cram cram 318903600.0 6378072.0 SC RUN 18732 2#2 0:50 A:91235181;C:80984947;G:84861359;T:61795663;N:26450 50       91235181 80984947 84861359 61795663 26450 ERX1468078 ERS1051426 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.57408   0.11398   0.87629   0.60954   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3038 3038 ERR1396818 ERX1468077 ERS1051425 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha B1 SAMEA3864291 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864291|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:55Z|INSDC last update:2016 02 03T09:48:20Z|INSDC status:public|Submitter Id:29904d70 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29904d70 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#1 15616869 Illumina sequencing of library 15616869 constructed from sample accession ERS1051425 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence ATCACG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#1.cram cram 411180300.0 8223606.0 SC RUN 18732 2#1 0:50 A:118946374;C:103897659;G:107565667;T:80736319;N:34281 50       118946374 103897659 107565667 80736319 34281 ERX1468077 ERS1051425 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.60674   0.11483   0.90258   0.54833   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3039 3039 ERR1396817 ERX1468076 ERS1051448 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 C7 SAMEA3864314 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864314|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:35Z|INSDC status:public|Submitter Id:2a85d100 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a85d100 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#24 15616955 Illumina sequencing of library 15616955 constructed from sample accession ERS1051448 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ATTCCT. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#24.cram cram 258624300.0 5172486.0 SC RUN 18732 1#24 0:50 A:74123846;C:66047722;G:64286422;T:54141623;N:24687 50       74123846 66047722 64286422 54141623 24687 ERX1468076 ERS1051448 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.62009   0.09612   0.88434   0.55718   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Embryo Imprecise All anatomical structures
3040 3040 ERR1396816 ERX1468075 ERS1051447 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 B12 SAMEA3864313 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864313|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:35Z|INSDC status:public|Submitter Id:2a7dbab0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a7dbab0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#23 15616943 Illumina sequencing of library 15616943 constructed from sample accession ERS1051447 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ACTGAT. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#23.cram cram 932669450.0 18653389.0 SC RUN 18732 1#23 0:50 A:270743929;C:232449590;G:241669732;T:187716399;N:89800 50       270743929 232449590 241669732 187716399 89800 ERX1468075 ERS1051447 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.58314   0.09813   0.87373   0.55534   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3041 3041 ERR1396815 ERX1468074 ERS1051446 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 B10 SAMEA3864312 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864312|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:34Z|INSDC status:public|Submitter Id:2a70e970 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a70e970 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#22 15616931 Illumina sequencing of library 15616931 constructed from sample accession ERS1051446 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GAGTGG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#22.cram cram 247740600.0 4954812.0 SC RUN 18732 1#22 0:50 A:70832472;C:61402287;G:66930146;T:48552217;N:23478 50       70832472 61402287 66930146 48552217 23478 ERX1468074 ERS1051446 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.60866   0.09645   0.87842   0.56581   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3042 3042 ERR1396814 ERX1468073 ERS1051445 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 B3 SAMEA3864311 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864311|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:34Z|INSDC status:public|Submitter Id:2a6aa7e0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a6aa7e0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#21 15616919 Illumina sequencing of library 15616919 constructed from sample accession ERS1051445 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence CGTACG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#21.cram cram 644730800.0 12894616.0 SC RUN 18732 1#21 0:50 A:183986486;C:164794735;G:168072875;T:127815308;N:61396 50       183986486 164794735 168072875 127815308 61396 ERX1468073 ERS1051445 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.62529   0.10255   0.87673   0.58496   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3043 3043 ERR1396813 ERX1468072 ERS1051444 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 A4 SAMEA3864310 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864310|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:33Z|INSDC status:public|Submitter Id:2a61a730 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a61a730 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#20 15616907 Illumina sequencing of library 15616907 constructed from sample accession ERS1051444 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GTTTCG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#20.cram cram 498997400.0 9979948.0 SC RUN 18732 1#20 0:50 A:140918075;C:126256924;G:131206962;T:100567098;N:48341 50       140918075 126256924 131206962 100567098 48341 ERX1468072 ERS1051444 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.54672   0.11372   0.8659   0.58386   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3044 3044 ERR1396812 ERX1468071 ERS1051443 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 A3 SAMEA3864309 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864309|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:32Z|INSDC status:public|Submitter Id:2a5a0610 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a5a0610 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#19 15616895 Illumina sequencing of library 15616895 constructed from sample accession ERS1051443 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GTGGCC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#19.cram cram 513060400.0 10261208.0 SC RUN 18732 1#19 0:50 A:143572990;C:132143361;G:136785883;T:100508957;N:49209 50       143572990 132143361 136785883 100508957 49209 ERX1468071 ERS1051443 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.55168   0.11683   0.86868   0.59303   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3045 3045 ERR1396811 ERX1468070 ERS1051442 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 A2 SAMEA3864308 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864308|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:32Z|INSDC status:public|Submitter Id:2a537660 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a537660 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#18 15616883 Illumina sequencing of library 15616883 constructed from sample accession ERS1051442 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GTGAAA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#18.cram cram 522864750.0 10457295.0 SC RUN 18732 1#18 0:50 A:152695334;C:132665110;G:137681171;T:99772629;N:50506 50       152695334 132665110 137681171 99772629 50506 ERX1468070 ERS1051442 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.54885   0.11528   0.88176   0.60373   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3046 3046 ERR1396810 ERX1468069 ERS1051441 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 A1 SAMEA3864307 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864307|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:31Z|INSDC status:public|Submitter Id:2a4c4a70 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a4c4a70 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#17 15616871 Illumina sequencing of library 15616871 constructed from sample accession ERS1051441 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GTCCGC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#17.cram cram 302165250.0 6043305.0 SC RUN 18732 1#17 0:50 A:85905345;C:81184773;G:78275206;T:56770744;N:29182 50       85905345 81184773 78275206 56770744 29182 ERX1468069 ERS1051441 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.50199   0.10346   0.90118   0.59572   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3047 3047 ERR1396809 ERX1468068 ERS1051440 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer C3 SAMEA3864306 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864306|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:31Z|INSDC status:public|Submitter Id:2a3ba8a0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a3ba8a0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#16 15616954 Illumina sequencing of library 15616954 constructed from sample accession ERS1051440 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence CCGTCC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#16.cram cram 252866050.0 5057321.0 SC RUN 18732 1#16 0:50 A:71001103;C:65550329;G:66199420;T:50091388;N:23810 50       71001103 65550329 66199420 50091388 23810 ERX1468068 ERS1051440 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.66563   0.10454   0.88239   0.53964   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3048 3048 ERR1396808 ERX1468067 ERS1051439 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer B4 SAMEA3864305 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864305|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:30Z|INSDC status:public|Submitter Id:2a319680 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a319680 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#15 15616942 Illumina sequencing of library 15616942 constructed from sample accession ERS1051439 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ATGTCA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#15.cram cram 274471250.0 5489425.0 SC RUN 18732 1#15 0:50 A:80060226;C:68799356;G:70635515;T:54950129;N:26024 50       80060226 68799356 70635515 54950129 26024 ERX1468067 ERS1051439 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.61964   0.09406   0.89402   0.55473   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3049 3049 ERR1396807 ERX1468066 ERS1051438 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer A7 SAMEA3864304 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864304|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:29Z|INSDC status:public|Submitter Id:2a2a6a90 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a2a6a90 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#14 15616930 Illumina sequencing of library 15616930 constructed from sample accession ERS1051438 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence AGTTCC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#14.cram cram 467847600.0 9356952.0 SC RUN 18732 1#14 0:50 A:134225837;C:118320475;G:121443773;T:93812243;N:45272 50       134225837 118320475 121443773 93812243 45272 ERX1468066 ERS1051438 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.64705   0.096   0.8983   0.56022   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3050 3050 ERR1396806 ERX1468065 ERS1051437 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer A1 SAMEA3864303 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864303|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:29Z|INSDC status:public|Submitter Id:2a238cc0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a238cc0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#13 15616918 Illumina sequencing of library 15616918 constructed from sample accession ERS1051437 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence AGTCAA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#13.cram cram 160243100.0 3204862.0 SC RUN 18732 1#13 0:50 A:46708835;C:40347424;G:41434539;T:31737029;N:15273 50       46708835 40347424 41434539 31737029 15273 ERX1468065 ERS1051437 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.65975   0.09405   0.90065   0.54178   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3051 3051 ERR1396805 ERX1468064 ERS1051436 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer C1 SAMEA3864302 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864302|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:28Z|INSDC status:public|Submitter Id:2a1b9d80 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a1b9d80 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#12 15616906 Illumina sequencing of library 15616906 constructed from sample accession ERS1051436 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence CTTGTA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#12.cram cram 378715650.0 7574313.0 SC RUN 18732 1#12 0:50 A:106991982;C:94292878;G:99663404;T:77730801;N:36585 50       106991982 94292878 99663404 77730801 36585 ERX1468064 ERS1051436 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.64513   0.11804   0.86525   0.55346   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3052 3052 ERR1396804 ERX1468063 ERS1051435 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer B3 SAMEA3864301 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864301|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:55Z|INSDC last update:2016 02 03T09:48:28Z|INSDC status:public|Submitter Id:2a0d93c0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a0d93c0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#11 15616894 Illumina sequencing of library 15616894 constructed from sample accession ERS1051435 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GGCTAC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#11.cram cram 139094000.0 2781880.0 SC RUN 18732 1#11 0:50 A:39702275;C:35436377;G:36969525;T:26972594;N:13229 50       39702275 35436377 36969525 26972594 13229 ERX1468063 ERS1051435 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.60357   0.10386   0.88872   0.5774   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3053 3053 ERR1396803 ERX1468062 ERS1051434 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer A12 SAMEA3864300 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864300|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:27Z|INSDC status:public|Submitter Id:2a075230 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a075230 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#10 15616882 Illumina sequencing of library 15616882 constructed from sample accession ERS1051434 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence TAGCTT. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#10.cram cram 263295150.0 5265903.0 SC RUN 18732 1#10 0:50 A:75332297;C:66059671;G:68562462;T:53315439;N:25281 50       75332297 66059671 68562462 53315439 25281 ERX1468062 ERS1051434 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.61939   0.10112   0.89613   0.55542   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3054 3054 ERR1396802 ERX1468061 ERS1051433 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer A10 SAMEA3864299 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864299|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:26Z|INSDC status:public|Submitter Id:29ffff30 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29ffff30 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#9 15616870 Illumina sequencing of library 15616870 constructed from sample accession ERS1051433 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GATCAG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#9.cram cram 7506900.0 150138.0 SC RUN 18732 1#9 0:50 A:2194276;C:1883363;G:1959471;T:1468994;N:796 50       2194276 1883363 1959471 1468994 796 ERX1468061 ERS1051433 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.60026   0.10518   0.91106   0.55508   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3055 3055 ERR1396801 ERX1468060 ERS1051432 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha C1 SAMEA3864298 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864298|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:26Z|INSDC status:public|Submitter Id:29f306e0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29f306e0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#8 15616953 Illumina sequencing of library 15616953 constructed from sample accession ERS1051432 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ACTTGA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#8.cram cram 464447300.0 9288946.0 SC RUN 18732 1#8 0:50 A:136629424;C:120103988;G:117495447;T:90173901;N:44540 50       136629424 120103988 117495447 90173901 44540 ERX1468060 ERS1051432 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.51298   0.10188   0.88434   0.6034   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3056 3056 ERR1396800 ERX1468059 ERS1051431 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha A9 SAMEA3864297 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864297|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:25Z|INSDC status:public|Submitter Id:29e942e0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29e942e0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#7 15616941 Illumina sequencing of library 15616941 constructed from sample accession ERS1051431 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence CAGATC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#7.cram cram 294666500.0 5893330.0 SC RUN 18732 1#7 0:50 A:85765921;C:76239559;G:76452231;T:56180868;N:27921 50       85765921 76239559 76452231 56180868 27921 ERX1468059 ERS1051431 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.56455   0.10217   0.88286   0.60374   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3057 3057 ERR1396799 ERX1468058 ERS1051430 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha A6 SAMEA3864296 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864296|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:25Z|INSDC status:public|Submitter Id:29e06940 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29e06940 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#6 15616929 Illumina sequencing of library 15616929 constructed from sample accession ERS1051430 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GCCAAT. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#6.cram cram 239549350.0 4790987.0 SC RUN 18732 1#6 0:50 A:68726161;C:60828350;G:62739441;T:47232484;N:22914 50       68726161 60828350 62739441 47232484 22914 ERX1468058 ERS1051430 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.64469   0.1021   0.88878   0.58044   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3058 3058 ERR1396798 ERX1468057 ERS1051429 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha A1 SAMEA3864295 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864295|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:24Z|INSDC status:public|Submitter Id:29d74180 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29d74180 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#5 15616917 Illumina sequencing of library 15616917 constructed from sample accession ERS1051429 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ACAGTG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#5.cram cram 165341300.0 3306826.0 SC RUN 18732 1#5 0:50 A:47735538;C:41622088;G:43392205;T:32575765;N:15704 50       47735538 41622088 43392205 32575765 15704 ERX1468057 ERS1051429 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.64704   0.09836   0.90534   0.56172   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3059 3059 ERR1396797 ERX1468056 ERS1051428 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha B12 SAMEA3864294 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864294|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:23Z|INSDC status:public|Submitter Id:29cf7950 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29cf7950 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#4 15616905 Illumina sequencing of library 15616905 constructed from sample accession ERS1051428 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence TGACCA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#4.cram cram 401336200.0 8026724.0 SC RUN 18732 1#4 0:50 A:117609087;C:105872656;G:100576681;T:77238881;N:38895 50       117609087 105872656 100576681 77238881 38895 ERX1468056 ERS1051428 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.51741   0.10352   0.89749   0.58497   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3060 3060 ERR1396796 ERX1468055 ERS1051427 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha B10 SAMEA3864293 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864293|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:22Z|INSDC status:public|Submitter Id:29c84d60 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29c84d60 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#3 15616893 Illumina sequencing of library 15616893 constructed from sample accession ERS1051427 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence TTAGGC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#3.cram cram 214767600.0 4295352.0 SC RUN 18732 1#3 0:50 A:61527319;C:53911904;G:56445139;T:42862938;N:20300 50       61527319 53911904 56445139 42862938 20300 ERX1468055 ERS1051427 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.57363   0.11614   0.88487   0.61011   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3061 3061 ERR1396795 ERX1468054 ERS1051426 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha B7 SAMEA3864292 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864292|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:22Z|INSDC status:public|Submitter Id:29b1df30 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29b1df30 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#2 15616881 Illumina sequencing of library 15616881 constructed from sample accession ERS1051426 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence CGATGT. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#2.cram cram 326025150.0 6520503.0 SC RUN 18732 1#2 0:50 A:93261648;C:82767834;G:86798075;T:63166259;N:31334 50       93261648 82767834 86798075 63166259 31334 ERX1468054 ERS1051426 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.57333   0.11365   0.87422   0.60838   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3062 3062 ERR1396794 ERX1468053 ERS1051425 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha B1 SAMEA3864291 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864291|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:55Z|INSDC last update:2016 02 03T09:48:20Z|INSDC status:public|Submitter Id:29904d70 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29904d70 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#1 15616869 Illumina sequencing of library 15616869 constructed from sample accession ERS1051425 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ATCACG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#1.cram cram 419669000.0 8393380.0 SC RUN 18732 1#1 0:50 A:121378853;C:106010609;G:109826454;T:82412717;N:40367 50       121378853 106010609 109826454 82412717 40367 ERX1468053 ERS1051425 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.60815   0.11567   0.90289   0.5657   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
9764 9764 ERR3454281 ERX3476201 ERS360451 ERP116513 PRJEB33700 Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961 Other Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors. ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26       SAMEA2224102 SC ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:47:37Z|External Id:SAMEA2224102|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:47:37Z|INSDC status:public|Submitter Id:ZMP phenotype 32 4 sibling sc 2013 10 17T10:16:28Z 1727409|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically normal embryos from ZMP phenotype 32 clutch 4. A 5 base indexing sequence CAAGA is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 4 sibling sc 2013 10 17T10:16:28Z 1727409|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 sequencing ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 6 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP116513 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26     659815100.0 13196302.0 ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 6 0:50 A:163494131;C:142490716;G:153472608;T:200319869;N:37776 50       163494131 142490716 153472608 200319869 37776 ERX3476201 ERS360451 ERA2051096 CIRI-Inserm-U1111|European Nucleotide Archive CIRI-Inserm-U1111 1 0.00278   0.00206   0.99922   0.24031   50   T   under 1.2% mapping rate illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   France 2014-03-04 Hatching Embryo Whole Organism All anatomical structures
9765 9765 ERR3454280 ERX3476200 ERS360450 ERP116513 PRJEB33700 Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961 Other Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors. ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26       SAMEA2224101 SC ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:50:06Z|External Id:SAMEA2224101|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:50:06Z|INSDC status:public|Submitter Id:ZMP phenotype 32 4 mutant sc 2013 10 17T10:16:27Z 1727408|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically abnormal embryos from ZMP phenotype32 clutch 4. A 5 base indexing sequence CGCAA is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 4 mutant sc 2013 10 17T10:16:27Z 1727408|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 sequencing ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 5 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP116513 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26     1031629900.0 20632598.0 ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 5 0:50 A:266496533;C:234318648;G:214719546;T:316013013;N:82160 50       266496533 234318648 214719546 316013013 82160 ERX3476200 ERS360450 ERA2051096 CIRI-Inserm-U1111|European Nucleotide Archive CIRI-Inserm-U1111 1 0.003   0.00187   0.99902   0.27272   50   T   under 1.2% mapping rate illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   France 2014-03-04 Hatching Embryo Whole Organism All anatomical structures
9766 9766 ERR3454279 ERX3476199 ERS360449 ERP116513 PRJEB33700 Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961 Other Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors. ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26       SAMEA2224100 SC ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:49:06Z|External Id:SAMEA2224100|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:49:06Z|INSDC status:public|Submitter Id:ZMP phenotype 32 3 sibling sc 2013 10 17T10:16:26Z 1727407|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically normal embryos from ZMP phenotype 32 clutch 3. A 5 base indexing sequence GCACG is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 3 sibling sc 2013 10 17T10:16:26Z 1727407|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 sequencing ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 4 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP116513 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26     547730200.0 10954604.0 ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 4 0:50 A:142048050;C:118592881;G:112867934;T:174179317;N:42018 50       142048050 118592881 112867934 174179317 42018 ERX3476199 ERS360449 ERA2051096 CIRI-Inserm-U1111|European Nucleotide Archive CIRI-Inserm-U1111 1 0.00355   0.00226   0.99902   0.30487   50   T   under 1.2% mapping rate illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   France 2014-03-04 Hatching Embryo Whole Organism All anatomical structures
9767 9767 ERR3454278 ERX3476198 ERS360448 ERP116513 PRJEB33700 Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961 Other Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors. ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26       SAMEA2224099 SC ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:47:37Z|External Id:SAMEA2224099|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:47:37Z|INSDC status:public|Submitter Id:ZMP phenotype 32 3 mutant sc 2013 10 17T10:16:24Z 1727406|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 32 clutch 3. A 5 base indexing sequence CAGAG is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 3 mutant sc 2013 10 17T10:16:24Z 1727406|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 sequencing ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 3 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP116513 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26     844323050.0 16886461.0 ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 3 0:50 A:219263127;C:181661743;G:173433057;T:269898556;N:66567 50       219263127 181661743 173433057 269898556 66567 ERX3476198 ERS360448 ERA2051096 CIRI-Inserm-U1111|European Nucleotide Archive CIRI-Inserm-U1111 1 0.00523   0.00319   0.99892   0.2637   50   T   under 1.2% mapping rate illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   France 2014-03-04 Hatching Embryo Whole Organism All anatomical structures
9768 9768 ERR3454277 ERX3476197 ERS360447 ERP116513 PRJEB33700 Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961 Other Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors. ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26       SAMEA2224098 SC ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:50:06Z|External Id:SAMEA2224098|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:50:06Z|INSDC status:public|Submitter Id:ZMP phenotype 32 2 sibling sc 2013 10 17T10:16:23Z 1727405|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically normal embryos from ZMP phenotype 32 clutch 2. A 5 base indexing sequence AGAAG is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 2 sibling sc 2013 10 17T10:16:23Z 1727405|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 sequencing ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP116513 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26     600000000.0 12000000.0 ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 2 0:50 A:153130383;C:136248892;G:127363796;T:183213089;N:43840 50       153130383 136248892 127363796 183213089 43840 ERX3476197 ERS360447 ERA2051096 CIRI-Inserm-U1111|European Nucleotide Archive CIRI-Inserm-U1111 1 0.00372   0.00211   0.99888   0.31649   50   T   under 1.2% mapping rate illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   France 2014-03-04 Hatching Embryo Whole Organism All anatomical structures
9769 9769 ERR3454276 ERX3476196 ERS360446 ERP116513 PRJEB33700 Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961 Other Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors. ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26       SAMEA2224097 SC ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:49:06Z|External Id:SAMEA2224097|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:49:06Z|INSDC status:public|Submitter Id:ZMP phenotype 32 2 mutant sc 2013 10 17T10:16:20Z 1727404|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 32 clutch 2. A 5 base indexing sequence GAGGC is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 2 mutant sc 2013 10 17T10:16:20Z 1727404|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 sequencing ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP116513 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26     600000000.0 12000000.0 ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 1 0:50 A:153852410;C:135392627;G:125428239;T:185280608;N:46116 50       153852410 135392627 125428239 185280608 46116 ERX3476196 ERS360446 ERA2051096 CIRI-Inserm-U1111|European Nucleotide Archive CIRI-Inserm-U1111 1 0.00545   0.00291   0.9988   0.31681   50   T   under 1.2% mapping rate illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   France 2014-03-04 Hatching Embryo Whole Organism All anatomical structures
10649 10649 ERR406885 ERX373262 ERS391761 ERP004564 PRJEB5188 YD embryos 8 hpf 24 hpf 32 hpf E-MTAB-2194 Transcriptome Analysis Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.     Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 5s24 SAMEA2299303 CAS-MPG PICB ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299303|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:5s24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:5s24|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb                 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf E MTAB 2194:Unique sample ID.4 batchA 24hpf SP YD embryos 8 hpf 24 hpf 32 hpf Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:24 hour RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   ERP004564 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16 5s24.fq.gz fastq 584550600.0 11691012.0 E MTAB 2194:5s24.fq.gz 0:50 1:0 A:154602150;C:138134763;G:138628704;T:153175234;N:9749 50 0     154602150 138134763 138628704 153175234 9749 ERX373262 ERS391761 ERA280282 CAS-MPG PICB|ArrayExpress CAS-MPG PICB|ArrayExpress 1 0.9356   0.0996   0.68615   0.47069   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-04-01 Multi-stage Embryo Whole Organism All anatomical structures
10650 10650 ERR406893 ERX373261 ERS391760 ERP004564 PRJEB5188 YD embryos 8 hpf 24 hpf 32 hpf E-MTAB-2194 Transcriptome Analysis Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.     Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 5y32 SAMEA2299302 CAS-MPG PICB ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299302|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:5y32|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:5y32|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb                 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf E MTAB 2194:Unique sample ID.5 batchA 32hpf YD YD embryos 8 hpf 24 hpf 32 hpf Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 Experimental Factor: treatment:yolk|Experimental Factor: time:32 hour RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   ERP004564 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16 5y32.fq.gz fastq 528892950.0 10577859.0 E MTAB 2194:5y32.fq.gz 0:50 1:0 A:140383478;C:125036983;G:124119152;T:139344643;N:8694 50 0     140383478 125036983 124119152 139344643 8694 ERX373261 ERS391760 ERA280282 CAS-MPG PICB|ArrayExpress CAS-MPG PICB|ArrayExpress 1 0.93478   0.10542   0.68296   0.4795   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-04-01 Multi-stage Embryo Whole Organism All anatomical structures
10651 10651 ERR406898 ERX373260 ERS391759 ERP004564 PRJEB5188 YD embryos 8 hpf 24 hpf 32 hpf E-MTAB-2194 Transcriptome Analysis Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.     Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 6s24 SAMEA2299301 CAS-MPG PICB ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299301|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:6s24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:6s24|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb                 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf E MTAB 2194:Unique sample ID.10 batchB 24hpf SP YD embryos 8 hpf 24 hpf 32 hpf Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:24 hour RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   ERP004564 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16 6s24.fq.gz fastq 542771850.0 10855437.0 E MTAB 2194:6s24.fq.gz 0:50 1:0 A:142311943;C:129686202;G:129130172;T:141634727;N:8806 50 0     142311943 129686202 129130172 141634727 8806 ERX373260 ERS391759 ERA280282 CAS-MPG PICB|ArrayExpress CAS-MPG PICB|ArrayExpress 1 0.93717   0.09239   0.68876   0.46809   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-04-01 Multi-stage Embryo Whole Organism All anatomical structures
10652 10652 ERR406896 ERX373259 ERS391758 ERP004564 PRJEB5188 YD embryos 8 hpf 24 hpf 32 hpf E-MTAB-2194 Transcriptome Analysis Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.     Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 13y32 SAMEA2299300 CAS-MPG PICB ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299300|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:13y32|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:13y32|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb                 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf E MTAB 2194:Unique sample ID.18 batchC 32hpf YD YD embryos 8 hpf 24 hpf 32 hpf Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 Experimental Factor: treatment:yolk|Experimental Factor: time:32 hour RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   ERP004564 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16 13y32.fq.gz fastq 649898350.0 12997967.0 E MTAB 2194:13y32.fq.gz 0:50 1:0 A:169738689;C:156130165;G:155102788;T:168916174;N:10534 50 0     169738689 156130165 155102788 168916174 10534 ERX373259 ERS391758 ERA280282 CAS-MPG PICB|ArrayExpress CAS-MPG PICB|ArrayExpress 1 0.93898   0.08535   0.68217   0.47133   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-04-01 Multi-stage Embryo Whole Organism All anatomical structures
10653 10653 ERR406899 ERX373258 ERS391757 ERP004564 PRJEB5188 YD embryos 8 hpf 24 hpf 32 hpf E-MTAB-2194 Transcriptome Analysis Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.     Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 5s32 SAMEA2299299 CAS-MPG PICB ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299299|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:5s32|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:5s32|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb                 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf E MTAB 2194:Unique sample ID.6 batchA 32hpf SP YD embryos 8 hpf 24 hpf 32 hpf Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:32 hour RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   ERP004564 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16 5s32.fq.gz fastq 566813600.0 11336272.0 E MTAB 2194:5s32.fq.gz 0:50 1:0 A:149907366;C:134421172;G:133399280;T:149076590;N:9192 50 0     149907366 134421172 133399280 149076590 9192 ERX373258 ERS391757 ERA280282 CAS-MPG PICB|ArrayExpress CAS-MPG PICB|ArrayExpress 1 0.93497   0.10019   0.68379   0.4671   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-04-01 Multi-stage Embryo Whole Organism All anatomical structures
10654 10654 ERR406888 ERX373257 ERS391756 ERP004564 PRJEB5188 YD embryos 8 hpf 24 hpf 32 hpf E-MTAB-2194 Transcriptome Analysis Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.     Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 5y24 SAMEA2299298 CAS-MPG PICB ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299298|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:5y24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:5y24|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb                 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf E MTAB 2194:Unique sample ID.3 batchA 24hpf YD YD embryos 8 hpf 24 hpf 32 hpf Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 Experimental Factor: treatment:yolk|Experimental Factor: time:24 hour RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   ERP004564 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16 5y24.fq.gz fastq 578936250.0 11578725.0 E MTAB 2194:5y24.fq.gz 0:50 1:0 A:154884020;C:135497257;G:135214353;T:153331273;N:9347 50 0     154884020 135497257 135214353 153331273 9347 ERX373257 ERS391756 ERA280282 CAS-MPG PICB|ArrayExpress CAS-MPG PICB|ArrayExpress 1 0.9342   0.1106   0.67811   0.47685   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-04-01 Multi-stage Embryo Whole Organism All anatomical structures
10655 10655 ERR406887 ERX373256 ERS391755 ERP004564 PRJEB5188 YD embryos 8 hpf 24 hpf 32 hpf E-MTAB-2194 Transcriptome Analysis Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.     Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 13s24 SAMEA2299297 CAS-MPG PICB ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299297|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:13s24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:13s24|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb                 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf E MTAB 2194:Unique sample ID.16 batchC 24hpf SP YD embryos 8 hpf 24 hpf 32 hpf Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:24 hour RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   ERP004564 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16 13s24.fq.gz fastq 837415050.0 16748301.0 E MTAB 2194:13s24.fq.gz 0:50 1:0 A:217172462;C:202556518;G:201365353;T:216307386;N:13331 50 0     217172462 202556518 201365353 216307386 13331 ERX373256 ERS391755 ERA280282 CAS-MPG PICB|ArrayExpress CAS-MPG PICB|ArrayExpress 1 0.93888   0.07561   0.6899   0.46646   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-04-01 Multi-stage Embryo Whole Organism All anatomical structures
10656 10656 ERR406894 ERX373255 ERS391754 ERP004564 PRJEB5188 YD embryos 8 hpf 24 hpf 32 hpf E-MTAB-2194 Transcriptome Analysis Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.     Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 6y24 SAMEA2299296 CAS-MPG PICB ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299296|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:6y24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:6y24|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb                 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf E MTAB 2194:Unique sample ID.9 batchB 24hpf YD YD embryos 8 hpf 24 hpf 32 hpf Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 Experimental Factor: treatment:yolk|Experimental Factor: time:24 hour RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   ERP004564 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16 6y24.fq.gz fastq 569424550.0 11388491.0 E MTAB 2194:6y24.fq.gz 0:50 1:0 A:149287318;C:136121879;G:135445765;T:148560272;N:9316 50 0     149287318 136121879 135445765 148560272 9316 ERX373255 ERS391754 ERA280282 CAS-MPG PICB|ArrayExpress CAS-MPG PICB|ArrayExpress 1 0.93486   0.0893   0.68751   0.46133   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-04-01 Multi-stage Embryo Whole Organism All anatomical structures
10657 10657 ERR406895 ERX373254 ERS391753 ERP004564 PRJEB5188 YD embryos 8 hpf 24 hpf 32 hpf E-MTAB-2194 Transcriptome Analysis Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.     Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 13s8 SAMEA2299295 CAS-MPG PICB ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299295|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:13s8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:13s8|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb                 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf E MTAB 2194:Unique sample ID.14 batchC 8hpf SP YD embryos 8 hpf 24 hpf 32 hpf Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:8 hour RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   ERP004564 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16 13s8.fq.gz fastq 532141500.0 10642830.0 E MTAB 2194:13s8.fq.gz 0:50 1:0 A:139773245;C:127051350;G:126773752;T:138534560;N:8593 50 0     139773245 127051350 126773752 138534560 8593 ERX373254 ERS391753 ERA280282 CAS-MPG PICB|ArrayExpress CAS-MPG PICB|ArrayExpress 1 0.93506   0.0742   0.74748   0.47765   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-04-01 Multi-stage Embryo Whole Organism All anatomical structures
10658 10658 ERR406891 ERX373253 ERS391752 ERP004564 PRJEB5188 YD embryos 8 hpf 24 hpf 32 hpf E-MTAB-2194 Transcriptome Analysis Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.     Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 6s8 SAMEA2299294 CAS-MPG PICB ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299294|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:6s8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:6s8|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb                 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf E MTAB 2194:Unique sample ID.8 batchB 8hpf SP YD embryos 8 hpf 24 hpf 32 hpf Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:8 hour RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   ERP004564 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16 6s8.fq.gz fastq 477620550.0 9552411.0 E MTAB 2194:6s8.fq.gz 0:50 1:0 A:127095393;C:112660046;G:111717464;T:126139686;N:7961 50 0     127095393 112660046 111717464 126139686 7961 ERX373253 ERS391752 ERA280282 CAS-MPG PICB|ArrayExpress CAS-MPG PICB|ArrayExpress 1 0.93605   0.08112   0.74552   0.46821   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-04-01 Multi-stage Embryo Whole Organism All anatomical structures
10659 10659 ERR406886 ERX373252 ERS391751 ERP004564 PRJEB5188 YD embryos 8 hpf 24 hpf 32 hpf E-MTAB-2194 Transcriptome Analysis Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.     Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 6y8 SAMEA2299293 CAS-MPG PICB ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299293|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:6y8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:6y8|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb                 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf E MTAB 2194:Unique sample ID.7 batchB 8hpf YD YD embryos 8 hpf 24 hpf 32 hpf Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 Experimental Factor: treatment:yolk|Experimental Factor: time:8 hour RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   ERP004564 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16 6y8.fq.gz fastq 508637450.0 10172749.0 E MTAB 2194:6y8.fq.gz 0:50 1:0 A:135377293;C:119833844;G:119447157;T:133970958;N:8198 50 0     135377293 119833844 119447157 133970958 8198 ERX373252 ERS391751 ERA280282 CAS-MPG PICB|ArrayExpress CAS-MPG PICB|ArrayExpress 1 0.93203   0.07833   0.73744   0.47586   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-04-01 Multi-stage Embryo Whole Organism All anatomical structures
10660 10660 ERR406892 ERX373251 ERS391750 ERP004564 PRJEB5188 YD embryos 8 hpf 24 hpf 32 hpf E-MTAB-2194 Transcriptome Analysis Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.     Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 6y32 SAMEA2299292 CAS-MPG PICB ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:37Z|External Id:SAMEA2299292|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:37Z|INSDC status:public|Submitter Id:E MTAB 2194:6y32|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:6y32|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb                 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf E MTAB 2194:Unique sample ID.11 batchB 32hpf YD YD embryos 8 hpf 24 hpf 32 hpf Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 Experimental Factor: treatment:yolk|Experimental Factor: time:32 hour RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   ERP004564 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16 6y32.fq.gz fastq 568482400.0 11369648.0 E MTAB 2194:6y32.fq.gz 0:50 1:0 A:149679881;C:135411801;G:134312216;T:149069222;N:9280 50 0     149679881 135411801 134312216 149069222 9280 ERX373251 ERS391750 ERA280282 CAS-MPG PICB|ArrayExpress CAS-MPG PICB|ArrayExpress 1 0.93184   0.104   0.68128   0.47652   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-04-01 Multi-stage Embryo Whole Organism All anatomical structures
10661 10661 ERR406897 ERX373250 ERS391749 ERP004564 PRJEB5188 YD embryos 8 hpf 24 hpf 32 hpf E-MTAB-2194 Transcriptome Analysis Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.     Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 5y8 SAMEA2299291 CAS-MPG PICB ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:37Z|External Id:SAMEA2299291|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:37Z|INSDC status:public|Submitter Id:E MTAB 2194:5y8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:5y8|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb                 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf E MTAB 2194:Unique sample ID.1 batchA 8hpf YD YD embryos 8 hpf 24 hpf 32 hpf Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 Experimental Factor: treatment:yolk|Experimental Factor: time:8 hour RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   ERP004564 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16 5y8.fq.gz fastq 497573200.0 9951464.0 E MTAB 2194:5y8.fq.gz 0:50 1:0 A:134128000;C:115688460;G:114668036;T:133080206;N:8498 50 0     134128000 115688460 114668036 133080206 8498 ERX373250 ERS391749 ERA280282 CAS-MPG PICB|ArrayExpress CAS-MPG PICB|ArrayExpress 1 0.93519   0.07057   0.73511   0.47977   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-04-01 Multi-stage Embryo Whole Organism All anatomical structures
10662 10662 ERR406889 ERX373249 ERS391748 ERP004564 PRJEB5188 YD embryos 8 hpf 24 hpf 32 hpf E-MTAB-2194 Transcriptome Analysis Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.     Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 13s32 SAMEA2299290 CAS-MPG PICB ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:37Z|External Id:SAMEA2299290|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:37Z|INSDC status:public|Submitter Id:E MTAB 2194:13s32|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:13s32|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb                 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf E MTAB 2194:Unique sample ID.19 batchC 32hpf SP YD embryos 8 hpf 24 hpf 32 hpf Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:32 hour RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   ERP004564 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16 13s32.fq.gz fastq 637724150.0 12754483.0 E MTAB 2194:13s32.fq.gz 0:50 1:0 A:165500205;C:154383334;G:152953181;T:164877160;N:10270 50 0     165500205 154383334 152953181 164877160 10270 ERX373249 ERS391748 ERA280282 CAS-MPG PICB|ArrayExpress CAS-MPG PICB|ArrayExpress 1 0.93998   0.08954   0.68146   0.4729   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-04-01 Multi-stage Embryo Whole Organism All anatomical structures
10663 10663 ERR406890 ERX373248 ERS391747 ERP004564 PRJEB5188 YD embryos 8 hpf 24 hpf 32 hpf E-MTAB-2194 Transcriptome Analysis Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.     Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 13y24 SAMEA2299289 CAS-MPG PICB ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:26Z|External Id:SAMEA2299289|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:26Z|INSDC status:public|Submitter Id:E MTAB 2194:13y24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:13y24|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb                 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf E MTAB 2194:Unique sample ID.15 batchC 24hpf YD YD embryos 8 hpf 24 hpf 32 hpf Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 Experimental Factor: treatment:yolk|Experimental Factor: time:24 hour RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   ERP004564 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16 13y24.fq.gz fastq 834725800.0 16694516.0 E MTAB 2194:13y24.fq.gz 0:50 1:0 A:216896952;C:201332171;G:200308143;T:216174965;N:13569 50 0     216896952 201332171 200308143 216174965 13569 ERX373248 ERS391747 ERA280282 CAS-MPG PICB|ArrayExpress CAS-MPG PICB|ArrayExpress 1 0.9358   0.07569   0.68757   0.46994   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-04-01 Multi-stage Embryo Whole Organism All anatomical structures
10664 10664 ERR406900 ERX373247 ERS391746 ERP004564 PRJEB5188 YD embryos 8 hpf 24 hpf 32 hpf E-MTAB-2194 Transcriptome Analysis Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.     Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 13y8 SAMEA2299288 CAS-MPG PICB ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:26Z|External Id:SAMEA2299288|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:26Z|INSDC status:public|Submitter Id:E MTAB 2194:13y8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:13y8|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb                 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf E MTAB 2194:Unique sample ID.13 batchC 8hpf YD YD embryos 8 hpf 24 hpf 32 hpf Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 Experimental Factor: treatment:yolk|Experimental Factor: time:8 hour RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   ERP004564 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16 13y8.fq.gz fastq 457245150.0 9144903.0 E MTAB 2194:13y8.fq.gz 0:50 1:0 A:119648940;C:109589521;G:109491446;T:118507707;N:7536 50 0     119648940 109589521 109491446 118507707 7536 ERX373247 ERS391746 ERA280282 CAS-MPG PICB|ArrayExpress CAS-MPG PICB|ArrayExpress 1 0.93146   0.0681   0.73718   0.47464   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-04-01 Multi-stage Embryo Whole Organism All anatomical structures
10665 10665 ERR406884 ERX373246 ERS391745 ERP004564 PRJEB5188 YD embryos 8 hpf 24 hpf 32 hpf E-MTAB-2194 Transcriptome Analysis Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.     Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 6s32 SAMEA2299287 CAS-MPG PICB ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:26Z|External Id:SAMEA2299287|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:26Z|INSDC status:public|Submitter Id:E MTAB 2194:6s32|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:6s32|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb                 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf E MTAB 2194:Unique sample ID.12 batchB 32hpf SP YD embryos 8 hpf 24 hpf 32 hpf Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:32 hour RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   ERP004564 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16 6s32.fq.gz fastq 652353200.0 13047064.0 E MTAB 2194:6s32.fq.gz 0:50 1:0 A:170844587;C:156203331;G:155264927;T:170029850;N:10505 50 0     170844587 156203331 155264927 170029850 10505 ERX373246 ERS391745 ERA280282 CAS-MPG PICB|ArrayExpress CAS-MPG PICB|ArrayExpress 1 0.93785   0.09102   0.68554   0.46397   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-04-01 Multi-stage Embryo Whole Organism All anatomical structures
10666 10666 ERR406901 ERX373245 ERS391744 ERP004564 PRJEB5188 YD embryos 8 hpf 24 hpf 32 hpf E-MTAB-2194 Transcriptome Analysis Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.     Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 5s8 SAMEA2299286 CAS-MPG PICB ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:26Z|External Id:SAMEA2299286|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:26Z|INSDC status:public|Submitter Id:E MTAB 2194:5s8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:5s8|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb                 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf E MTAB 2194:Unique sample ID.2 batchA 8hpf SP YD embryos 8 hpf 24 hpf 32 hpf Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:8 hour RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   ERP004564 Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16 5s8.fq.gz fastq 359298500.0 7185970.0 E MTAB 2194:5s8.fq.gz 0:50 1:0 A:96450828;C:83805020;G:83440885;T:95595844;N:5923 50 0     96450828 83805020 83440885 95595844 5923 ERX373245 ERS391744 ERA280282 CAS-MPG PICB|ArrayExpress CAS-MPG PICB|ArrayExpress 1 0.93524   0.07491   0.73312   0.47914   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-04-01 Multi-stage Embryo Whole Organism All anatomical structures
15070 15070 ERR12476466 ERX11852287 ERS17743541 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1219 from a cross with a starved father 1219 Starved 1219S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:193 277029 1219S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1219S_S12_L003_R1_001.fastq.gz fastq 97592891.0 1298822.0 ena RUN TAB 15 01 2024 21:42:36:193 277030 0:75.14 A:34708924;C:19086989;G:21325291;T:22442527;N:29160 75       34708924 19086989 21325291 22442527 29160 ERX11852287 ERS17743541 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15071 15071 ERR12476447 ERX11852268 ERS17743536 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1203 from a cross with a fed father 1203 Fed 1203F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:179 276991 1203F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1203F_S5_L004_R1_001.fastq.gz fastq 92134036.0 1226106.0 ena RUN TAB 15 01 2024 21:42:36:179 276992 0:75.14 A:33032252;C:17497320;G:19713134;T:21873197;N:18133 75       33032252 17497320 19713134 21873197 18133 ERX11852268 ERS17743536 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15072 15072 ERR12476437 ERX11852258 ERS17743534 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1118 from a cross with a fed father 1118 Fed 1118F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:172 276971 1118F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1118F_S9_L002_R1_001.fastq.gz fastq 98606332.0 1311676.0 ena RUN TAB 15 01 2024 21:42:36:172 276972 0:75.18 A:35097475;C:19013865;G:21072825;T:23400976;N:21191 75       35097475 19013865 21072825 23400976 21191 ERX11852258 ERS17743534 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15073 15073 ERR12476468 ERX11852289 ERS17743542 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a fed father 1242D Fed 1242FD   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:194 277033 1242FD 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242FD_S13_L001_R1_001.fastq.gz fastq 89342488.0 1186885.0 ena RUN TAB 15 01 2024 21:42:36:194 277034 0:75.27 A:31174342;C:17129181;G:18704493;T:22323017;N:11455 75       31174342 17129181 18704493 22323017 11455 ERX11852289 ERS17743542 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15074 15074 ERR12476438 ERX11852259 ERS17743534 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1118 from a cross with a fed father 1118 Fed 1118F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:173 276973 1118F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1118F_S9_L003_R1_001.fastq.gz fastq 98443412.0 1309747.0 ena RUN TAB 15 01 2024 21:42:36:173 276974 0:75.16 A:35171021;C:18991511;G:20974950;T:23280285;N:25645 75       35171021 18991511 20974950 23280285 25645 ERX11852259 ERS17743534 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15075 15075 ERR12476442 ERX11852263 ERS17743535 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1118 from a cross with a starved father 1118 Starved 1118S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:176 276981 1118S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1118S_S10_L003_R1_001.fastq.gz fastq 98865255.0 1315357.0 ena RUN TAB 15 01 2024 21:42:36:176 276982 0:75.16 A:34981471;C:19126822;G:21304286;T:23427226;N:25450 75       34981471 19126822 21304286 23427226 25450 ERX11852263 ERS17743535 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15076 15076 ERR12476467 ERX11852288 ERS17743541 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1219 from a cross with a starved father 1219 Starved 1219S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:193 277031 1219S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1219S_S12_L004_R1_001.fastq.gz fastq 88230016.0 1174256.0 ena RUN TAB 15 01 2024 21:42:36:194 277032 0:75.14 A:31409300;C:17203675;G:19284478;T:20309174;N:23389 75       31409300 17203675 19284478 20309174 23389 ERX11852288 ERS17743541 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15077 15077 ERR12476470 ERX11852291 ERS17743542 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a fed father 1242D Fed 1242FD   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:195 277037 1242FD 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242FD_S13_L003_R1_001.fastq.gz fastq 93375090.0 1240903.0 ena RUN TAB 15 01 2024 21:42:36:196 277038 0:75.25 A:32510114;C:17950920;G:19575617;T:23324862;N:13577 75       32510114 17950920 19575617 23324862 13577 ERX11852291 ERS17743542 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15078 15078 ERR12476436 ERX11852257 ERS17743534 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1118 from a cross with a fed father 1118 Fed 1118F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:171 276969 1118F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1118F_S9_L001_R1_001.fastq.gz fastq 94258948.0 1253428.0 ena RUN TAB 15 01 2024 21:42:36:171 276970 0:75.20 A:33713614;C:18157124;G:20086205;T:22277451;N:24554 75       33713614 18157124 20086205 22277451 24554 ERX11852257 ERS17743534 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15079 15079 ERR12476452 ERX11852273 ERS17743538 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1210 from a cross with a fed father 1210 Fed 1210F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:183 277001 1210F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1210F_S7_L001_R1_001.fastq.gz fastq 96414625.0 1283672.0 ena RUN TAB 15 01 2024 21:42:36:183 277002 0:75.11 A:35605799;C:18366729;G:20807908;T:21594044;N:40145 75       35605799 18366729 20807908 21594044 40145 ERX11852273 ERS17743538 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15080 15080 ERR12476475 ERX11852296 ERS17743544 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a fed father 1242E Fed 1242FE   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:199 277047 1242FE 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242FE_S15_L004_R1_001.fastq.gz fastq 99581325.0 1325945.0 ena RUN TAB 15 01 2024 21:42:36:199 277048 0:75.10 A:36802442;C:18868511;G:20958294;T:22926783;N:25295 75       36802442 18868511 20958294 22926783 25295 ERX11852296 ERS17743544 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15082 15082 ERR12476473 ERX11852294 ERS17743544 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a fed father 1242E Fed 1242FE   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:198 277043 1242FE 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242FE_S15_L002_R1_001.fastq.gz fastq 111191327.0 1479982.0 ena RUN TAB 15 01 2024 21:42:36:198 277044 0:75.13 A:40873794;C:21118758;G:23508088;T:25663516;N:27171 75       40873794 21118758 23508088 25663516 27171 ERX11852294 ERS17743544 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15083 15083 ERR12476472 ERX11852293 ERS17743544 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a fed father 1242E Fed 1242FE   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:197 277041 1242FE 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242FE_S15_L001_R1_001.fastq.gz fastq 105936834.0 1409443.0 ena RUN TAB 15 01 2024 21:42:36:197 277042 0:75.16 A:39084749;C:20103850;G:22336806;T:24384711;N:26718 75       39084749 20103850 22336806 24384711 26718 ERX11852293 ERS17743544 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15084 15084 ERR12476455 ERX11852276 ERS17743538 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1210 from a cross with a fed father 1210 Fed 1210F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:185 277007 1210F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1210F_S7_L004_R1_001.fastq.gz fastq 91003627.0 1212716.0 ena RUN TAB 15 01 2024 21:42:36:185 277008 0:75.04 A:33677348;C:17299066;G:19585548;T:20403064;N:38601 75       33677348 17299066 19585548 20403064 38601 ERX11852276 ERS17743538 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15085 15085 ERR12476450 ERX11852271 ERS17743537 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1203 from a cross with a starved father 1203 Starved 1203S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:181 276997 1203S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1203S_S6_L003_R1_001.fastq.gz fastq 93998632.0 1251284.0 ena RUN TAB 15 01 2024 21:42:36:182 276998 0:75.12 A:33959433;C:18143368;G:20041026;T:21824242;N:30563 75       33959433 18143368 20041026 21824242 30563 ERX11852271 ERS17743537 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15086 15086 ERR12476446 ERX11852267 ERS17743536 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1203 from a cross with a fed father 1203 Fed 1203F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:178 276989 1203F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1203F_S5_L003_R1_001.fastq.gz fastq 102209965.0 1360067.0 ena RUN TAB 15 01 2024 21:42:36:179 276990 0:75.15 A:36554629;C:19466103;G:21890238;T:24276196;N:22799 75       36554629 19466103 21890238 24276196 22799 ERX11852267 ERS17743536 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15087 15087 ERR12476458 ERX11852279 ERS17743539 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1210 from a cross with a starved father 1210 Starved 1210S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:187 277013 1210S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1210S_S8_L003_R1_001.fastq.gz fastq 109602092.0 1466517.0 ena RUN TAB 15 01 2024 21:42:36:187 277014 0:74.74 A:42677564;C:20838229;G:24413347;T:21498031;N:174921 74       42677564 20838229 24413347 21498031 174921 ERX11852279 ERS17743539 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15088 15088 ERR12476453 ERX11852274 ERS17743538 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1210 from a cross with a fed father 1210 Fed 1210F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:183 277003 1210F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1210F_S7_L002_R1_001.fastq.gz fastq 100538748.0 1339248.0 ena RUN TAB 15 01 2024 21:42:36:184 277004 0:75.07 A:36966184;C:19156780;G:21758079;T:22618911;N:38794 75       36966184 19156780 21758079 22618911 38794 ERX11852274 ERS17743538 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15089 15089 ERR12476460 ERX11852281 ERS17743540 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1219 from a cross with a fed father 1219 Fed 1219F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:188 277017 1219F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1219F_S11_L001_R1_001.fastq.gz fastq 102219114.0 1358650.0 ena RUN TAB 15 01 2024 21:42:36:189 277018 0:75.24 A:35886099;C:19931420;G:22057068;T:24325918;N:18609 75       35886099 19931420 22057068 24325918 18609 ERX11852281 ERS17743540 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15090 15090 ERR12476451 ERX11852272 ERS17743537 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1203 from a cross with a starved father 1203 Starved 1203S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:182 276999 1203S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1203S_S6_L004_R1_001.fastq.gz fastq 84880221.0 1129985.0 ena RUN TAB 15 01 2024 21:42:36:182 277000 0:75.12 A:30708531;C:16338743;G:18094345;T:19712906;N:25696 75       30708531 16338743 18094345 19712906 25696 ERX11852272 ERS17743537 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15091 15091 ERR12476441 ERX11852262 ERS17743535 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1118 from a cross with a starved father 1118 Starved 1118S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:175 276979 1118S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1118S_S10_L002_R1_001.fastq.gz fastq 99340604.0 1321436.0 ena RUN TAB 15 01 2024 21:42:36:175 276980 0:75.18 A:34996267;C:19218610;G:21486623;T:23616635;N:22469 75       34996267 19218610 21486623 23616635 22469 ERX11852262 ERS17743535 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15092 15092 ERR12476440 ERX11852261 ERS17743535 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1118 from a cross with a starved father 1118 Starved 1118S   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:174 276977 1118S 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1118S_S10_L001_R1_001.fastq.gz fastq 94655454.0 1258724.0 ena RUN TAB 15 01 2024 21:42:36:175 276978 0:75.20 A:33514914;C:18282513;G:20410100;T:22427564;N:20363 75       33514914 18282513 20410100 22427564 20363 ERX11852261 ERS17743535 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15093 15093 ERR12476469 ERX11852290 ERS17743542 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a fed father 1242D Fed 1242FD   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:195 277035 1242FD 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242FD_S13_L002_R1_001.fastq.gz fastq 93346527.0 1240308.0 ena RUN TAB 15 01 2024 21:42:36:195 277036 0:75.26 A:32401771;C:17929540;G:19597511;T:23408465;N:9240 75       32401771 17929540 19597511 23408465 9240 ERX11852290 ERS17743542 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15094 15094 ERR12476462 ERX11852283 ERS17743540 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1219 from a cross with a fed father 1219 Fed 1219F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:190 277021 1219F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1219F_S11_L003_R1_001.fastq.gz fastq 106745726.0 1419461.0 ena RUN TAB 15 01 2024 21:42:36:190 277022 0:75.20 A:37396946;C:20851140;G:23075114;T:25400364;N:22162 75       37396946 20851140 23075114 25400364 22162 ERX11852283 ERS17743540 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15095 15095 ERR12476479 ERX11852300 ERS17743543 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a starved father 1242D Starved 1242SD   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:202 277055 1242SD 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242SD_S14_L004_R1_001.fastq.gz fastq 85586412.0 1137781.0 ena RUN TAB 15 01 2024 21:42:36:202 277056 0:75.22 A:29963542;C:16621745;G:18219345;T:20761941;N:19839 75       29963542 16621745 18219345 20761941 19839 ERX11852300 ERS17743543 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15096 15096 ERR12476444 ERX11852265 ERS17743536 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1203 from a cross with a fed father 1203 Fed 1203F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:177 276985 1203F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1203F_S5_L001_R1_001.fastq.gz fastq 97624173.0 1298240.0 ena RUN TAB 15 01 2024 21:42:36:177 276986 0:75.20 A:34935070;C:18569640;G:20912883;T:23188491;N:18089 75       34935070 18569640 20912883 23188491 18089 ERX11852265 ERS17743536 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15097 15097 ERR12476471 ERX11852292 ERS17743542 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1242 from a cross with a fed father 1242D Fed 1242FD   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:196 277039 1242FD 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1242FD_S13_L004_R1_001.fastq.gz fastq 83383881.0 1108207.0 ena RUN TAB 15 01 2024 21:42:36:196 277040 0:75.24 A:29091135;C:15949002;G:17455499;T:20878004;N:10241 75       29091135 15949002 17455499 20878004 10241 ERX11852292 ERS17743542 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
15098 15098 ERR12476439 ERX11852260 ERS17743534 ERP156655 PRJEB71869 Effects of paternal starvation in the offspring development of zebrafish 33b9d14c-4211-4249-aede-f0f021d197e6 Other Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15   24 hpf embryo collected at 1118 from a cross with a fed father 1118 Fed 1118F   organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden                 NextSeq 500 sequencing ena EXPERIMENT TAB 15 01 2024 21:42:36:174 276975 1118F 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   ERP156655 NextSeq 500 sequencing ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 1118F_S9_L004_R1_001.fastq.gz fastq 88439160.0 1176751.0 ena RUN TAB 15 01 2024 21:42:36:174 276976 0:75.16 A:31652556;C:16996499;G:18832233;T:20937970;N:19902 75       31652556 16996499 18832233 20937970 19902 ERX11852260 ERS17743534 ERA27788968 University of Birmingham|European Nucleotide Archive University of Birmingham                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2024-01-15 Pharyngula Embryo Embryo Imprecise All anatomical structures

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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");;