RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

4,207 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "cDNA" and tissue_curation = "Whole Organism"

✎ View and edit SQL

This data as json, CSV (advanced)

devstage_curation >10

technology 8

experiment.platform 6

devstage_curation_coarse 5

experiment.library_strategy 2

experiment.library_source 2

tissue_curation_coarse 1

tissue_curation 1

  • Whole Organism · 4,207 ✖

experiment.library_selection 1

  • cDNA · 4,207 ✖

experiment.library_layout 1

  • SINGLE · 4,207 ✖
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
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
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
25273 25273 SRR25764091 SRX21486763 SRS18719063 SRP457108 PRJNA1009807 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [RNA Seq] GSE241752 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT bud 10 hpf RNA seq rep2 GSM7734768   source name:Gastrula|strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT|geo loc name:missing|collection date:missing WT bud 10 hpf RNA seq rep2 3’ adapters were trimmed using Trim Galore v0.6.4 with default settings retaining reads of length ≥20. Reads were aligned to the GRCz11 zebrafish genome using STAR v2.6.1c with the following parameters: outSAMtype BAM SortedByCoordinate outFilterMultimapNmax 1 outFilterMismatchNmax 1 quantMode TranscriptomeSAM GeneCounts alignEndsType Local seedSearchStartLmax 14 alignIntronMax 10000 outFilterIntronMotifs RemoveNoncanonicalUnannotated. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts. Assembly: GRCz11 Supplementary files format and content: csv; transcripts per million TPM counts per transcript in MANE annotation Gastrula unperturbed growth conditions in E3 medium for zebrafish embryos. 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform. Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT GSM7734768 GSM7734768: WT bud 10 hpf RNA seq rep2; Danio rerio; RNA Seq GSM7734768 r1 GSM7734768 1 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP457108     WT_mRNA_bud_2.fastq.gz fastq 2470912004.0 31168086.0 GSM7734768 r1 0:79.28 A:656817108;C:568241258;G:504262095;T:741507737;N:83806 79       656817108 568241258 504262095 741507737 83806 SRX21486763 SRS18719063 SRA1700431 Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry Max Planck Institute of Biochemistry 1 0.91479   0.27298   0.74231   0.57302   79   B   usable mapping rate illumina nextseq unknown small_rna unknown bulk bulk bulk   Germany 2023-08-28 Gastrula Embryo Whole Organism All anatomical structures
25274 25274 SRR25764092 SRX21486762 SRS18719064 SRP457108 PRJNA1009807 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [RNA Seq] GSE241752 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT bud 10 hpf RNA seq rep1 GSM7734767   source name:Gastrula|strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT|geo loc name:missing|collection date:missing WT bud 10 hpf RNA seq rep1 3’ adapters were trimmed using Trim Galore v0.6.4 with default settings retaining reads of length ≥20. Reads were aligned to the GRCz11 zebrafish genome using STAR v2.6.1c with the following parameters: outSAMtype BAM SortedByCoordinate outFilterMultimapNmax 1 outFilterMismatchNmax 1 quantMode TranscriptomeSAM GeneCounts alignEndsType Local seedSearchStartLmax 14 alignIntronMax 10000 outFilterIntronMotifs RemoveNoncanonicalUnannotated. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts. Assembly: GRCz11 Supplementary files format and content: csv; transcripts per million TPM counts per transcript in MANE annotation Gastrula unperturbed growth conditions in E3 medium for zebrafish embryos. 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform. Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT GSM7734767 GSM7734767: WT bud 10 hpf RNA seq rep1; Danio rerio; RNA Seq GSM7734767 r1 GSM7734767 1 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP457108     WT_mRNA_bud_1.fastq.gz fastq 2153494756.0 27140032.0 GSM7734767 r1 0:79.35 A:560793143;C:508962676;G:445126772;T:638539310;N:72855 79       560793143 508962676 445126772 638539310 72855 SRX21486762 SRS18719064 SRA1700431 Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry Max Planck Institute of Biochemistry 1 0.88728   0.25493   0.74369   0.56589   80   B   usable mapping rate illumina nextseq unknown small_rna unknown bulk bulk bulk   Germany 2023-08-28 Gastrula Embryo Whole Organism All anatomical structures
25275 25275 SRR25764093 SRX21486761 SRS18719061 SRP457108 PRJNA1009807 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [RNA Seq] GSE241752 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT sphere 4 hpf RNA seq rep2 GSM7734766   source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT|geo loc name:missing|collection date:missing WT sphere 4 hpf RNA seq rep2 3’ adapters were trimmed using Trim Galore v0.6.4 with default settings retaining reads of length ≥20. Reads were aligned to the GRCz11 zebrafish genome using STAR v2.6.1c with the following parameters: outSAMtype BAM SortedByCoordinate outFilterMultimapNmax 1 outFilterMismatchNmax 1 quantMode TranscriptomeSAM GeneCounts alignEndsType Local seedSearchStartLmax 14 alignIntronMax 10000 outFilterIntronMotifs RemoveNoncanonicalUnannotated. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts. Assembly: GRCz11 Supplementary files format and content: csv; transcripts per million TPM counts per transcript in MANE annotation Blastula unperturbed growth conditions in E3 medium for zebrafish embryos. 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform. Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT GSM7734766 GSM7734766: WT sphere 4 hpf RNA seq rep2; Danio rerio; RNA Seq GSM7734766 r1 GSM7734766 1 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP457108     WT_mRNA_sphere_2.fastq.gz fastq 2455317157.0 30934591.0 GSM7734766 r1 0:79.37 A:614860604;C:588586084;G:522132289;T:729655621;N:82559 79       614860604 588586084 522132289 729655621 82559 SRX21486761 SRS18719061 SRA1700431 Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry Max Planck Institute of Biochemistry 1 0.94124   0.10502   0.74876   0.57752   80   B   usable mapping rate illumina nextseq unknown small_rna unknown bulk bulk bulk   Germany 2023-08-28 Blastula Embryo Whole Organism All anatomical structures
25276 25276 SRR25764094 SRX21486760 SRS18719060 SRP457108 PRJNA1009807 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [RNA Seq] GSE241752 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT sphere 4 hpf RNA seq rep1 GSM7734765   source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT|geo loc name:missing|collection date:missing WT sphere 4 hpf RNA seq rep1 3’ adapters were trimmed using Trim Galore v0.6.4 with default settings retaining reads of length ≥20. Reads were aligned to the GRCz11 zebrafish genome using STAR v2.6.1c with the following parameters: outSAMtype BAM SortedByCoordinate outFilterMultimapNmax 1 outFilterMismatchNmax 1 quantMode TranscriptomeSAM GeneCounts alignEndsType Local seedSearchStartLmax 14 alignIntronMax 10000 outFilterIntronMotifs RemoveNoncanonicalUnannotated. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts. Assembly: GRCz11 Supplementary files format and content: csv; transcripts per million TPM counts per transcript in MANE annotation Blastula unperturbed growth conditions in E3 medium for zebrafish embryos. 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform. Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT GSM7734765 GSM7734765: WT sphere 4 hpf RNA seq rep1; Danio rerio; RNA Seq GSM7734765 r1 GSM7734765 1 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP457108     WT_mRNA_sphere_1.fastq.gz fastq 2399640874.0 30232118.0 GSM7734765 r1 0:79.37 A:589069860;C:593745131;G:511439690;T:705305674;N:80519 79       589069860 593745131 511439690 705305674 80519 SRX21486760 SRS18719060 SRA1700431 Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry Max Planck Institute of Biochemistry 1 0.85882   0.11848   0.75122   0.5883   80   B   usable mapping rate illumina nextseq unknown small_rna unknown bulk bulk bulk   Germany 2023-08-28 Blastula Embryo Whole Organism All anatomical structures
28113 28113 SRR26209648 SRX21920662 SRS19005181 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 3 GSM7812991   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812991 GSM7812991: unDMSO t1 WT 3; Danio rerio; RNA Seq GSM7812991 r1 GSM7812991 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A30_S48_L005_R1_001.fastq.gz fastq 616449359.0 6103459.0 GSM7812991 r1 0:101 A:152808626;C:149738763;G:141639387;T:172257280;N:5303 101       152808626 149738763 141639387 172257280 5303 SRX21920662 SRS19005181 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94246   0.08766   0.69443   0.4842   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28114 28114 SRR26209649 SRX21920662 SRS19005181 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 3 GSM7812991   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812991 GSM7812991: unDMSO t1 WT 3; Danio rerio; RNA Seq GSM7812991 r1 GSM7812991 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A30_S48_L006_R1_001.fastq.gz fastq 609999297.0 6039597.0 GSM7812991 r2 0:101 A:151226657;C:148143193;G:140088806;T:170530812;N:9829 101       151226657 148143193 140088806 170530812 9829 SRX21920662 SRS19005181 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94201   0.08569   0.69572   0.48692   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28115 28115 SRR26209650 SRX21920662 SRS19005181 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 3 GSM7812991   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812991 GSM7812991: unDMSO t1 WT 3; Danio rerio; RNA Seq GSM7812991 r1 GSM7812991 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A30_S48_L007_R1_001.fastq.gz fastq 543730470.0 5383470.0 GSM7812991 r3 0:101 A:134685766;C:132190291;G:124881864;T:151967639;N:4910 101       134685766 132190291 124881864 151967639 4910 SRX21920662 SRS19005181 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.9431   0.08733   0.69524   0.48528   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28116 28116 SRR26209651 SRX21920662 SRS19005181 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 3 GSM7812991   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812991 GSM7812991: unDMSO t1 WT 3; Danio rerio; RNA Seq GSM7812991 r1 GSM7812991 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A30_S16_L007_R1_001.fastq.gz fastq 649354149.0 6429249.0 GSM7812991 r4 0:101 A:160756303;C:158145998;G:149623680;T:180816390;N:11778 101       160756303 158145998 149623680 180816390 11778 SRX21920662 SRS19005181 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94438   0.08618   0.69473   0.48809   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28117 28117 SRR26209752 SRX21920662 SRS19005181 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 3 GSM7812991   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812991 GSM7812991: unDMSO t1 WT 3; Danio rerio; RNA Seq GSM7812991 r1 GSM7812991 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A30_S16_L008_R1_001.fastq.gz fastq 650450504.0 6440104.0 GSM7812991 r5 0:101 A:161054597;C:158340761;G:149784923;T:181251361;N:18862 101       161054597 158340761 149784923 181251361 18862 SRX21920662 SRS19005181 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94338   0.08713   0.6968   0.48443   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28118 28118 SRR26209652 SRX21920661 SRS19005180 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 2 GSM7812990   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812990 GSM7812990: unDMSO t1 WT 2; Danio rerio; RNA Seq GSM7812990 r1 GSM7812990 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A29_S46_L005_R1_001.fastq.gz fastq 593068162.0 5871962.0 GSM7812990 r1 0:101 A:147906639;C:143944406;G:137307101;T:163904929;N:5087 101       147906639 143944406 137307101 163904929 5087 SRX21920661 SRS19005180 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94371   0.06473   0.69378   0.47765   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28119 28119 SRR26209653 SRX21920661 SRS19005180 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 2 GSM7812990   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812990 GSM7812990: unDMSO t1 WT 2; Danio rerio; RNA Seq GSM7812990 r1 GSM7812990 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A29_S46_L006_R1_001.fastq.gz fastq 588323081.0 5824981.0 GSM7812990 r2 0:101 A:146630863;C:142829925;G:136124185;T:162728186;N:9922 101       146630863 142829925 136124185 162728186 9922 SRX21920661 SRS19005180 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94282   0.06357   0.69418   0.47665   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28120 28120 SRR26209654 SRX21920661 SRS19005180 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 2 GSM7812990   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812990 GSM7812990: unDMSO t1 WT 2; Danio rerio; RNA Seq GSM7812990 r1 GSM7812990 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A29_S46_L007_R1_001.fastq.gz fastq 521265747.0 5161047.0 GSM7812990 r3 0:101 A:129905878;C:126622019;G:120526207;T:144206853;N:4790 101       129905878 126622019 120526207 144206853 4790 SRX21920661 SRS19005180 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94508   0.06499   0.69367   0.4834   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28121 28121 SRR26209655 SRX21920661 SRS19005180 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 2 GSM7812990   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812990 GSM7812990: unDMSO t1 WT 2; Danio rerio; RNA Seq GSM7812990 r1 GSM7812990 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A29_S26_L007_R1_001.fastq.gz fastq 623834580.0 6176580.0 GSM7812990 r4 0:101 A:155642981;C:151651242;G:144681951;T:171847192;N:11214 101       155642981 151651242 144681951 171847192 11214 SRX21920661 SRS19005180 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94531   0.06514   0.69225   0.48187   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28122 28122 SRR26209656 SRX21920661 SRS19005180 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 2 GSM7812990   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812990 GSM7812990: unDMSO t1 WT 2; Danio rerio; RNA Seq GSM7812990 r1 GSM7812990 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A29_S26_L008_R1_001.fastq.gz fastq 622155960.0 6159960.0 GSM7812990 r5 0:101 A:155145221;C:151231599;G:144290581;T:171470641;N:17918 101       155145221 151231599 144290581 171470641 17918 SRX21920661 SRS19005180 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94319   0.06413   0.69449   0.48159   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28123 28123 SRR26209657 SRX21920660 SRS19005179 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 1 GSM7812989   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812989 GSM7812989: unDMSO t1 WT 1; Danio rerio; RNA Seq GSM7812989 r1 GSM7812989 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A28_S45_L005_R1_001.fastq.gz fastq 602520550.0 5965550.0 GSM7812989 r1 0:101 A:149619230;C:146559346;G:139674646;T:166662143;N:5185 101       149619230 146559346 139674646 166662143 5185 SRX21920660 SRS19005179 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94449   0.06296   0.69487   0.48   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28124 28124 SRR26209658 SRX21920660 SRS19005179 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 1 GSM7812989   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812989 GSM7812989: unDMSO t1 WT 1; Danio rerio; RNA Seq GSM7812989 r1 GSM7812989 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A28_S45_L006_R1_001.fastq.gz fastq 596942522.0 5910322.0 GSM7812989 r2 0:101 A:148193962;C:145221539;G:138267073;T:165249833;N:10115 101       148193962 145221539 138267073 165249833 10115 SRX21920660 SRS19005179 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.9446   0.06327   0.69562   0.48183   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28125 28125 SRR26209659 SRX21920660 SRS19005179 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 1 GSM7812989   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812989 GSM7812989: unDMSO t1 WT 1; Danio rerio; RNA Seq GSM7812989 r1 GSM7812989 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A28_S45_L007_R1_001.fastq.gz fastq 532539064.0 5272664.0 GSM7812989 r3 0:101 A:132217323;C:129660296;G:123303893;T:147352732;N:4820 101       132217323 129660296 123303893 147352732 4820 SRX21920660 SRS19005179 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94579   0.06237   0.69554   0.46658   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28126 28126 SRR26209660 SRX21920660 SRS19005179 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 1 GSM7812989   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812989 GSM7812989: unDMSO t1 WT 1; Danio rerio; RNA Seq GSM7812989 r1 GSM7812989 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A28_S29_L007_R1_001.fastq.gz fastq 633337569.0 6270669.0 GSM7812989 r4 0:101 A:157286526;C:154336036;G:147137950;T:174565295;N:11762 101       157286526 154336036 147137950 174565295 11762 SRX21920660 SRS19005179 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94562   0.06294   0.69489   0.47406   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28127 28127 SRR26209661 SRX21920660 SRS19005179 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 1 GSM7812989   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812989 GSM7812989: unDMSO t1 WT 1; Danio rerio; RNA Seq GSM7812989 r1 GSM7812989 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A28_S29_L008_R1_001.fastq.gz fastq 636051540.0 6297540.0 GSM7812989 r5 0:101 A:157845668;C:154972063;G:147765532;T:175449801;N:18476 101       157845668 154972063 147765532 175449801 18476 SRX21920660 SRS19005179 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.9471   0.06288   0.69536   0.4797   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28128 28128 SRR26209662 SRX21920659 SRS19005178 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 3 GSM7812988   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812988 GSM7812988: unDMSO t1 K2 3; Danio rerio; RNA Seq GSM7812988 r1 GSM7812988 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A36_S54_L005_R1_001.fastq.gz fastq 674188635.0 6675135.0 GSM7812988 r1 0:101 A:173104307;C:161481671;G:152542615;T:187053812;N:6230 101       173104307 161481671 152542615 187053812 6230 SRX21920659 SRS19005178 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94039   0.07795   0.69877   0.48386   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28129 28129 SRR26209663 SRX21920659 SRS19005178 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 3 GSM7812988   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812988 GSM7812988: unDMSO t1 K2 3; Danio rerio; RNA Seq GSM7812988 r1 GSM7812988 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A36_S54_L006_R1_001.fastq.gz fastq 667048339.0 6604439.0 GSM7812988 r2 0:101 A:171316049;C:159786547;G:150743446;T:185190228;N:12069 101       171316049 159786547 150743446 185190228 12069 SRX21920659 SRS19005178 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94064   0.07881   0.69767   0.48162   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28130 28130 SRR26209664 SRX21920659 SRS19005178 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 3 GSM7812988   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812988 GSM7812988: unDMSO t1 K2 3; Danio rerio; RNA Seq GSM7812988 r1 GSM7812988 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A36_S54_L007_R1_001.fastq.gz fastq 596645683.0 5907383.0 GSM7812988 r3 0:101 A:153131508;C:143126741;G:134745614;T:165635953;N:5867 101       153131508 143126741 134745614 165635953 5867 SRX21920659 SRS19005178 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94156   0.07795   0.69751   0.4833   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28131 28131 SRR26209665 SRX21920659 SRS19005178 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 3 GSM7812988   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812988 GSM7812988: unDMSO t1 K2 3; Danio rerio; RNA Seq GSM7812988 r1 GSM7812988 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A36_S12_L007_R1_001.fastq.gz fastq 712385926.0 7053326.0 GSM7812988 r4 0:101 A:183100436;C:171026605;G:161510527;T:196734608;N:13750 101       183100436 171026605 161510527 196734608 13750 SRX21920659 SRS19005178 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94298   0.07892   0.6997   0.48331   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28132 28132 SRR26209666 SRX21920659 SRS19005178 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 3 GSM7812988   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812988 GSM7812988: unDMSO t1 K2 3; Danio rerio; RNA Seq GSM7812988 r1 GSM7812988 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A36_S12_L008_R1_001.fastq.gz fastq 714661355.0 7075855.0 GSM7812988 r5 0:101 A:183454698;C:171554090;G:162064705;T:197567065;N:20797 101       183454698 171554090 162064705 197567065 20797 SRX21920659 SRS19005178 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94316   0.07877   0.70051   0.48354   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28133 28133 SRR26209667 SRX21920658 SRS19005177 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 2 GSM7812987   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812987 GSM7812987: unDMSO t1 K2 2; Danio rerio; RNA Seq GSM7812987 r1 GSM7812987 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A35_S53_L005_R1_001.fastq.gz fastq 611900723.0 6058423.0 GSM7812987 r1 0:101 A:154668392;C:147817141;G:139653400;T:169756342;N:5448 101       154668392 147817141 139653400 169756342 5448 SRX21920658 SRS19005177 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94636   0.08022   0.69962   0.48201   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28134 28134 SRR26209668 SRX21920658 SRS19005177 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 2 GSM7812987   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812987 GSM7812987: unDMSO t1 K2 2; Danio rerio; RNA Seq GSM7812987 r1 GSM7812987 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A35_S53_L006_R1_001.fastq.gz fastq 602971818.0 5970018.0 GSM7812987 r2 0:101 A:152346877;C:145640105;G:137576284;T:167398281;N:10271 101       152346877 145640105 137576284 167398281 10271 SRX21920658 SRS19005177 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94549   0.08086   0.69781   0.47842   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28135 28135 SRR26209669 SRX21920658 SRS19005177 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 2 GSM7812987   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812987 GSM7812987: unDMSO t1 K2 2; Danio rerio; RNA Seq GSM7812987 r1 GSM7812987 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A35_S53_L007_R1_001.fastq.gz fastq 539246575.0 5339075.0 GSM7812987 r3 0:101 A:136317506;C:130390122;G:122927887;T:149606028;N:5032 101       136317506 130390122 122927887 149606028 5032 SRX21920658 SRS19005177 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94653   0.08075   0.69704   0.48374   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28136 28136 SRR26209670 SRX21920658 SRS19005177 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 2 GSM7812987   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812987 GSM7812987: unDMSO t1 K2 2; Danio rerio; RNA Seq GSM7812987 r1 GSM7812987 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A35_S47_L007_R1_001.fastq.gz fastq 643197593.0 6368293.0 GSM7812987 r4 0:101 A:162743675;C:155711536;G:147135700;T:177594459;N:12223 101       162743675 155711536 147135700 177594459 12223 SRX21920658 SRS19005177 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94757   0.08023   0.70055   0.48458   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28137 28137 SRR26209671 SRX21920658 SRS19005177 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 2 GSM7812987   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812987 GSM7812987: unDMSO t1 K2 2; Danio rerio; RNA Seq GSM7812987 r1 GSM7812987 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A35_S47_L008_R1_001.fastq.gz fastq 644356063.0 6379763.0 GSM7812987 r5 0:101 A:162915651;C:155935181;G:147406641;T:178079118;N:19472 101       162915651 155935181 147406641 178079118 19472 SRX21920658 SRS19005177 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94817   0.08218   0.70017   0.48286   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28138 28138 SRR26209672 SRX21920657 SRS19005176 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 1 GSM7812986   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812986 GSM7812986: unDMSO t1 K2 1; Danio rerio; RNA Seq GSM7812986 r1 GSM7812986 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A34_S52_L005_R1_001.fastq.gz fastq 615996374.0 6098974.0 GSM7812986 r1 0:101 A:156934542;C:147417998;G:139301915;T:172336421;N:5498 101       156934542 147417998 139301915 172336421 5498 SRX21920657 SRS19005176 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94179   0.07628   0.69512   0.48041   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures

Next page

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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");;