run_metadata
1,196 rows where devstage_curation = "Multi-stage" and tissue_curation = "Whole Organism"
This data as json, CSV (advanced)
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 5026 | 5026 | ERR1706529 | ERX1776763 | ERS1227000 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 C9 | SAMEA4055890 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000051|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055890|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:24:00Z|INSDC status:public|Submitter Id:d7b0b9c0 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7b0b9c0 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#23 | 17117131 | Illumina sequencing of library 17117131 constructed from sample accession ERS1227000 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence ACTGAT. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#23.cram | cram | 743861850.0 | 4959079.0 | SC RUN 20417 1#23 | 0:75 1:75 | A:188550455;C:183533703;G:184197810;T:187506925;N:72957 | 75 | 75 | 188550455 | 183533703 | 184197810 | 187506925 | 72957 | ERX1776763 | ERS1227000 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.96302 | 0.96531 | 0.19802 | 0.19492 | 0.73298 | 0.73312 | 0.57888 | 0.58087 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||
| 5027 | 5027 | ERR1706528 | ERX1776762 | ERS1226979 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 C5 | SAMEA4055869 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000050|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055869|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:23:35Z|INSDC status:public|Submitter Id:d7a93fb0 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7a93fb0 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#22 | 17117119 | Illumina sequencing of library 17117119 constructed from sample accession ERS1226979 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence GAGTGG. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#22.cram | cram | 1375781700.0 | 9171878.0 | SC RUN 20417 1#22 | 0:75 1:75 | A:332899223;C:355056529;G:356526015;T:331162157;N:137776 | 75 | 75 | 332899223 | 355056529 | 356526015 | 331162157 | 137776 | ERX1776762 | ERS1226979 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.96835 | 0.97046 | 0.22984 | 0.22663 | 0.753 | 0.75491 | 0.45383 | 0.51122 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||
| 5028 | 5028 | ERR1706527 | ERX1776761 | ERS1226967 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 C4 | SAMEA4055857 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000049|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055857|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:23:22Z|INSDC status:public|Submitter Id:d7a1c5a0 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7a1c5a0 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#21 | 17117107 | Illumina sequencing of library 17117107 constructed from sample accession ERS1226967 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence CGTACG. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#21.cram | cram | 1984245000.0 | 13228300.0 | SC RUN 20417 1#21 | 0:75 1:75 | A:468564557;C:523118317;G:524896332;T:467470998;N:194796 | 75 | 75 | 468564557 | 523118317 | 524896332 | 467470998 | 194796 | ERX1776761 | ERS1226967 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.97058 | 0.97302 | 0.22668 | 0.22361 | 0.76122 | 0.76319 | 0.6447 | 0.64941 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||
| 5029 | 5029 | ERR1706526 | ERX1776760 | ERS1226955 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 C1 | SAMEA4055845 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000048|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055845|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:23:08Z|INSDC status:public|Submitter Id:d799d660 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d799d660 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#20 | 17117095 | Illumina sequencing of library 17117095 constructed from sample accession ERS1226955 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence GTTTCG. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#20.cram | cram | 1202223750.0 | 8014825.0 | SC RUN 20417 1#20 | 0:75 1:75 | A:288569721;C:312339594;G:312724314;T:288471735;N:118386 | 75 | 75 | 288569721 | 312339594 | 312724314 | 288471735 | 118386 | ERX1776760 | ERS1226955 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.9701 | 0.97208 | 0.23493 | 0.2308 | 0.75856 | 0.75893 | 0.51831 | 0.52827 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||
| 5030 | 5030 | ERR1706525 | ERX1776759 | ERS1226947 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 B11 | SAMEA4055837 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000047|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055837|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:23:00Z|INSDC status:public|Submitter Id:d7920e30 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7920e30 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#19 | 17117083 | Illumina sequencing of library 17117083 constructed from sample accession ERS1226947 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence GTGGCC. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#19.cram | cram | 1177752450.0 | 7851683.0 | SC RUN 20417 1#19 | 0:75 1:75 | A:311936666;C:276917229;G:278564226;T:310217446;N:116883 | 75 | 75 | 311936666 | 276917229 | 278564226 | 310217446 | 116883 | ERX1776759 | ERS1226947 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.95807 | 0.96101 | 0.1671 | 0.16592 | 0.72389 | 0.72521 | 0.53692 | 0.53083 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||
| 5031 | 5031 | ERR1706524 | ERX1776758 | ERS1226939 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 B10 | SAMEA4055829 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000046|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055829|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:22:51Z|INSDC status:public|Submitter Id:d788e670 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d788e670 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#18 | 17117071 | Illumina sequencing of library 17117071 constructed from sample accession ERS1226939 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence GTGAAA. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#18.cram | cram | 1306412850.0 | 8709419.0 | SC RUN 20417 1#18 | 0:75 1:75 | A:348858023;C:304800763;G:306149463;T:346474389;N:130212 | 75 | 75 | 348858023 | 304800763 | 306149463 | 346474389 | 130212 | ERX1776758 | ERS1226939 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.95746 | 0.9601 | 0.16534 | 0.1628 | 0.72297 | 0.72247 | 0.52807 | 0.52513 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||
| 5032 | 5032 | ERR1706523 | ERX1776757 | ERS1226931 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 B9 | SAMEA4055821 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000045|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055821|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:22:43Z|INSDC status:public|Submitter Id:d780d020 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d780d020 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#17 | 17117059 | Illumina sequencing of library 17117059 constructed from sample accession ERS1226931 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence GTCCGC. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#17.cram | cram | 943334550.0 | 6288897.0 | SC RUN 20417 1#17 | 0:75 1:75 | A:250576062;C:221289820;G:222449063;T:248930088;N:89517 | 75 | 75 | 250576062 | 221289820 | 222449063 | 248930088 | 89517 | ERX1776757 | ERS1226931 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.95898 | 0.9615 | 0.16669 | 0.16433 | 0.72636 | 0.7262 | 0.53064 | 0.52544 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||
| 5033 | 5033 | ERR1706522 | ERX1776756 | ERS1226910 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 B6 | SAMEA4055800 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000044|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055800|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:22:20Z|INSDC status:public|Submitter Id:d778e0e0 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d778e0e0 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#16 | 17117142 | Illumina sequencing of library 17117142 constructed from sample accession ERS1226910 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence CCGTCC. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#16.cram | cram | 1397786700.0 | 9318578.0 | SC RUN 20417 1#16 | 0:75 1:75 | A:370541493;C:328697895;G:330649047;T:367761875;N:136390 | 75 | 75 | 370541493 | 328697895 | 330649047 | 367761875 | 136390 | ERX1776756 | ERS1226910 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.95779 | 0.96097 | 0.15701 | 0.15529 | 0.72462 | 0.72425 | 0.53437 | 0.53651 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||
| 5034 | 5034 | ERR1706521 | ERX1776755 | ERS1226903 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 B4 | SAMEA4055793 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000043|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055793|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:22:11Z|INSDC status:public|Submitter Id:d7713fc0 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7713fc0 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#15 | 17117130 | Illumina sequencing of library 17117130 constructed from sample accession ERS1226903 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence ATGTCA. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#15.cram | cram | 2090642550.0 | 13937617.0 | SC RUN 20417 1#15 | 0:75 1:75 | A:573574606;C:473115476;G:474137164;T:569607223;N:208081 | 75 | 75 | 573574606 | 473115476 | 474137164 | 569607223 | 208081 | ERX1776755 | ERS1226903 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.95314 | 0.95602 | 0.13917 | 0.13779 | 0.71605 | 0.7161 | 0.5009 | 0.49877 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||
| 5035 | 5035 | ERR1706520 | ERX1776754 | ERS1226896 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 B3 | SAMEA4055786 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000042|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055786|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:22:03Z|INSDC status:public|Submitter Id:d7697790 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7697790 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#14 | 17117118 | Illumina sequencing of library 17117118 constructed from sample accession ERS1226896 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence AGTTCC. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#14.cram | cram | 1829182200.0 | 12194548.0 | SC RUN 20417 1#14 | 0:75 1:75 | A:501496169;C:412501773;G:416194477;T:498811651;N:178130 | 75 | 75 | 501496169 | 412501773 | 416194477 | 498811651 | 178130 | ERX1776754 | ERS1226896 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.95118 | 0.95498 | 0.14818 | 0.14602 | 0.71431 | 0.71478 | 0.49278 | 0.4993 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||
| 5036 | 5036 | ERR1706519 | ERX1776753 | ERS1226884 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 B2 | SAMEA4055774 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000041|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055774|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:21:52Z|INSDC status:public|Submitter Id:d761fd80 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d761fd80 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#13 | 17117106 | Illumina sequencing of library 17117106 constructed from sample accession ERS1226884 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence AGTCAA. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#13.cram | cram | 969474450.0 | 6463163.0 | SC RUN 20417 1#13 | 0:75 1:75 | A:262909712;C:222419636;G:222543360;T:261505885;N:95857 | 75 | 75 | 262909712 | 222419636 | 222543360 | 261505885 | 95857 | ERX1776753 | ERS1226884 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.95449 | 0.95866 | 0.15114 | 0.14937 | 0.71437 | 0.71465 | 0.51271 | 0.50858 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||
| 5037 | 5037 | ERR1706518 | ERX1776752 | ERS1226870 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 B1 | SAMEA4055760 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000040|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055760|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:21:36Z|INSDC status:public|Submitter Id:d75a3550 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d75a3550 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#12 | 17117094 | Illumina sequencing of library 17117094 constructed from sample accession ERS1226870 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence CTTGTA. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#12.cram | cram | 1454862600.0 | 9699084.0 | SC RUN 20417 1#12 | 0:75 1:75 | A:398496982;C:328471618;G:330736633;T:397014742;N:142625 | 75 | 75 | 398496982 | 328471618 | 330736633 | 397014742 | 142625 | ERX1776752 | ERS1226870 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.95557 | 0.95961 | 0.13233 | 0.1312 | 0.71441 | 0.71488 | 0.49023 | 0.48445 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||
| 5038 | 5038 | ERR1706517 | ERX1776751 | ERS1226860 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 A12 | SAMEA4055750 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000039|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055750|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:21:28Z|INSDC status:public|Submitter Id:d7529430 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish non transgenic actin:prl3.1 sibling embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7529430 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#11 | 17117082 | Illumina sequencing of library 17117082 constructed from sample accession ERS1226860 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence GGCTAC. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#11.cram | cram | 1746393900.0 | 11642626.0 | SC RUN 20417 1#11 | 0:75 1:75 | A:431979433;C:441330253;G:441743262;T:431172392;N:168560 | 75 | 75 | 431979433 | 441330253 | 441743262 | 431172392 | 168560 | ERX1776751 | ERS1226860 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.96506 | 0.9668 | 0.22176 | 0.21891 | 0.74491 | 0.74621 | 0.60192 | 0.59716 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||
| 5039 | 5039 | ERR1706516 | ERX1776750 | ERS1226849 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 A11 | SAMEA4055739 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000038|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055739|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:21:18Z|INSDC status:public|Submitter Id:d74a56d0 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish non transgenic actin:prl3.1 sibling embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d74a56d0 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#10 | 17117070 | Illumina sequencing of library 17117070 constructed from sample accession ERS1226849 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence TAGCTT. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#10.cram | cram | 1489471050.0 | 9929807.0 | SC RUN 20417 1#10 | 0:75 1:75 | A:370582953;C:374410965;G:374249460;T:370079632;N:148040 | 75 | 75 | 370582953 | 374410965 | 374249460 | 370079632 | 148040 | ERX1776750 | ERS1226849 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.96529 | 0.96757 | 0.21607 | 0.21231 | 0.74272 | 0.7432 | 0.59703 | 0.6019 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||
| 5040 | 5040 | ERR1706515 | ERX1776749 | ERS1226835 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 A9 | SAMEA4055725 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055725|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:21:06Z|INSDC status:public|Submitter Id:d7428ea0 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish non transgenic actin:prl3.1 sibling embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7428ea0 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#9 | 17117058 | Illumina sequencing of library 17117058 constructed from sample accession ERS1226835 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence GATCAG. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#9.cram | cram | 812740200.0 | 5418268.0 | SC RUN 20417 1#9 | 0:75 1:75 | A:212802181;C:193901585;G:194345487;T:211612018;N:78929 | 75 | 75 | 212802181 | 193901585 | 194345487 | 211612018 | 78929 | ERX1776749 | ERS1226835 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.95783 | 0.95996 | 0.17262 | 0.1685 | 0.72413 | 0.72448 | 0.53944 | 0.53954 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||
| 5041 | 5041 | ERR1706514 | ERX1776748 | ERS1226824 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 A8 | SAMEA4055714 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000036|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055714|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:20:58Z|INSDC status:public|Submitter Id:d73ac670 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish non transgenic actin:prl3.1 sibling embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d73ac670 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#8 | 17117141 | Illumina sequencing of library 17117141 constructed from sample accession ERS1226824 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence ACTTGA. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#8.cram | cram | 1782401400.0 | 11882676.0 | SC RUN 20417 1#8 | 0:75 1:75 | A:458909593;C:432851102;G:434061292;T:456406952;N:172461 | 75 | 75 | 458909593 | 432851102 | 434061292 | 456406952 | 172461 | ERX1776748 | ERS1226824 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.96096 | 0.96367 | 0.18551 | 0.18292 | 0.73413 | 0.73373 | 0.56474 | 0.56438 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||
| 5042 | 5042 | ERR1706513 | ERX1776747 | ERS1226813 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 A7 | SAMEA4055703 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000035|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055703|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:20:49Z|INSDC status:public|Submitter Id:d7332550 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish non transgenic actin:prl3.1 sibling embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7332550 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#7 | 17117129 | Illumina sequencing of library 17117129 constructed from sample accession ERS1226813 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence CAGATC. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#7.cram | cram | 396397350.0 | 2642649.0 | SC RUN 20417 1#7 | 0:75 1:75 | A:103468605;C:95292253;G:94558692;T:103038245;N:39555 | 75 | 75 | 103468605 | 95292253 | 94558692 | 103038245 | 39555 | ERX1776747 | ERS1226813 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.96013 | 0.96276 | 0.17171 | 0.16938 | 0.72941 | 0.73046 | 0.54526 | 0.54527 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||
| 5043 | 5043 | ERR1706512 | ERX1776746 | ERS1226790 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 A6 | SAMEA4055680 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000034|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055680|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:20:34Z|INSDC status:public|Submitter Id:d72b5d20 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish non transgenic actin:prl3.1 sibling embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d72b5d20 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#6 | 17117117 | Illumina sequencing of library 17117117 constructed from sample accession ERS1226790 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence GCCAAT. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#6.cram | cram | 652493400.0 | 4349956.0 | SC RUN 20417 1#6 | ERX1776746 | ERS1226790 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.94432 | 0.94163 | 0.16831 | 0.16496 | 0.72912 | 0.72766 | 0.50382 | 0.5065 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 5044 | 5044 | ERR1706511 | ERX1776745 | ERS1226779 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 A5 | SAMEA4055669 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000033|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055669|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:20:26Z|INSDC status:public|Submitter Id:d7219920 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish non transgenic actin:prl3.1 sibling embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7219920 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#5 | 17117105 | Illumina sequencing of library 17117105 constructed from sample accession ERS1226779 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence ACAGTG. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#5.cram | cram | 825205650.0 | 5501371.0 | SC RUN 20417 1#5 | 0:75 1:75 | A:224928393;C:188238841;G:188933086;T:223024865;N:80465 | 75 | 75 | 224928393 | 188238841 | 188933086 | 223024865 | 80465 | ERX1776745 | ERS1226779 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.95709 | 0.96033 | 0.14048 | 0.13863 | 0.71887 | 0.71987 | 0.49099 | 0.49207 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||
| 5045 | 5045 | ERR1706510 | ERX1776744 | ERS1226767 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 A4 | SAMEA4055657 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000032|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055657|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:20:16Z|INSDC status:public|Submitter Id:d71934b0 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish non transgenic actin:prl3.1 sibling embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d71934b0 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#4 | 17117093 | Illumina sequencing of library 17117093 constructed from sample accession ERS1226767 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence TGACCA. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#4.cram | cram | 767189250.0 | 5114595.0 | SC RUN 20417 1#4 | 0:75 1:75 | A:210673766;C:173125942;G:174062852;T:209253897;N:72793 | 75 | 75 | 210673766 | 173125942 | 174062852 | 209253897 | 72793 | ERX1776744 | ERS1226767 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.95581 | 0.95773 | 0.11947 | 0.11773 | 0.72103 | 0.72178 | 0.4674 | 0.46869 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||
| 5046 | 5046 | ERR1706509 | ERX1776743 | ERS1226757 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 A3 | SAMEA4055647 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000031|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055647|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:20:08Z|INSDC status:public|Submitter Id:d7092f20 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish non transgenic actin:prl3.1 sibling embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7092f20 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#3 | 17117081 | Illumina sequencing of library 17117081 constructed from sample accession ERS1226757 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence TTAGGC. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#3.cram | cram | 776002350.0 | 5173349.0 | SC RUN 20417 1#3 | 0:75 1:75 | A:207553748;C:180473885;G:180618978;T:207278008;N:77731 | 75 | 75 | 207553748 | 180473885 | 180618978 | 207278008 | 77731 | ERX1776743 | ERS1226757 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.96457 | 0.96611 | 0.23757 | 0.23414 | 0.74507 | 0.74497 | 0.55158 | 0.55086 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||
| 5047 | 5047 | ERR1706508 | ERX1776742 | ERS1226745 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 A2 | SAMEA4055635 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000030|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055635|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:19:59Z|INSDC status:public|Submitter Id:d6f77be0 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish non transgenic actin:prl3.1 sibling embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d6f77be0 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#2 | 17117069 | Illumina sequencing of library 17117069 constructed from sample accession ERS1226745 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence CGATGT. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#2.cram | cram | 581391900.0 | 3875946.0 | SC RUN 20417 1#2 | 0:75 1:75 | A:156042125;C:134966129;G:135462829;T:154862718;N:58099 | 75 | 75 | 156042125 | 134966129 | 135462829 | 154862718 | 58099 | ERX1776742 | ERS1226745 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.9582 | 0.96234 | 0.1297 | 0.12747 | 0.72863 | 0.72949 | 0.48838 | 0.48132 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||
| 5048 | 5048 | ERR1706507 | ERX1776741 | ERS1226722 | ERP016002 | PRJEB14364 | Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos | Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266 | Transcriptome Analysis | RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling. | ArrayExpress:E ERAD 507 | zmp ph260 A1 | SAMEA4055612 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Segmentation:26+somites Pharyngula:Prim 5 ZFS:0000028 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055612|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:19:38Z|INSDC status:public|Submitter Id:d6e3f3e0 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish non transgenic actin:prl3.1 sibling embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d6e3f3e0 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed | Illumina HiSeq 2000 paired end sequencing | SC EXP 20417 1#1 | 17117057 | Illumina sequencing of library 17117057 constructed from sample accession ERS1226722 for study accession ERP016002. This is part of an Illumina multiplexed sequencing run 20417 1. This submission includes reads tagged with the sequence ATCACG. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP016002 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16 | 20417_1#1.cram | cram | 1233271650.0 | 8221811.0 | SC RUN 20417 1#1 | 0:75 1:75 | A:334336992;C:282740616;G:283953463;T:332113804;N:126775 | 75 | 75 | 334336992 | 282740616 | 283953463 | 332113804 | 126775 | ERX1776741 | ERS1226722 | ERA740537 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.95579 | 0.95701 | 0.15941 | 0.15689 | 0.71758 | 0.71709 | 0.4967 | 0.5163 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-06-28 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||
| 9825 | 9825 | ERR2102841 | ERX2160152 | ERS1883528 | ERP040145 | PRJEB37796 | Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | E-MTAB-5992 | Transcriptome Analysis | We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals | ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992 | Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 | N3 nabu RNA | SAMEA104224510 | Fundacao Champalimaud | ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224510|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N3 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N3 nabu RNA|strain:AB | Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | E MTAB 5992:N3 nabu RNA s | N3 nabu RNA s | Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 | Experimental Factor: compound:NaBu|Experimental Factor: dose:2 | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | ERP040145 | Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 | N3_R1_all.fastq.gz | fastq | 1410139550.0 | 18670564.0 | E MTAB 5992:N3 nabu RNA | 0:75.53 1:0 | A:353294009;C:340727934;G:322476371;T:393200193;N:441043 | 75 | 0 | 353294009 | 340727934 | 322476371 | 393200193 | 441043 | ERX2160152 | ERS1883528 | ERA1011308 | Fundacao Champalimaud|European Nucleotide Archive | Fundacao Champalimaud|European Nucleotide Archive | 1 | 0.95434 | 0.08906 | 0.66935 | 0.47788 | 76 | B | usable mapping rate | illumina | early_illumina | unknown | random_priming | trueseq | bulk | unknown | unknown | Portugal | 2017-08-23 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||||||
| 9826 | 9826 | ERR2102840 | ERX2160151 | ERS1883527 | ERP040145 | PRJEB37796 | Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | E-MTAB-5992 | Transcriptome Analysis | We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals | ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992 | Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 | N2 nabu RNA | SAMEA104224509 | Fundacao Champalimaud | ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224509|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N2 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N2 nabu RNA|strain:AB | Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | E MTAB 5992:N2 nabu RNA s | N2 nabu RNA s | Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 | Experimental Factor: compound:NaBu|Experimental Factor: dose:2 | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | ERP040145 | Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 | N2_R1_all.fastq.gz | fastq | 1478621168.0 | 19576865.0 | E MTAB 5992:N2 nabu RNA | 0:75.53 1:0 | A:369453299;C:359092235;G:341176884;T:408389810;N:508940 | 75 | 0 | 369453299 | 359092235 | 341176884 | 408389810 | 508940 | ERX2160151 | ERS1883527 | ERA1011308 | Fundacao Champalimaud|European Nucleotide Archive | Fundacao Champalimaud|European Nucleotide Archive | 1 | 0.95582 | 0.08202 | 0.67718 | 0.47812 | 76 | B | usable mapping rate | illumina | early_illumina | unknown | random_priming | trueseq | bulk | unknown | unknown | Portugal | 2017-08-23 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||||||
| 9827 | 9827 | ERR2102839 | ERX2160150 | ERS1883526 | ERP040145 | PRJEB37796 | Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | E-MTAB-5992 | Transcriptome Analysis | We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals | ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992 | Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 | N1 nabu RNA | SAMEA104224508 | Fundacao Champalimaud | ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224508|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N1 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N1 nabu RNA|strain:AB | Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | E MTAB 5992:N1 nabu RNA s | N1 nabu RNA s | Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 | Experimental Factor: compound:NaBu|Experimental Factor: dose:2 | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | ERP040145 | Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 | N1_R1_all.fastq.gz | fastq | 1531713181.0 | 20277882.0 | E MTAB 5992:N1 nabu RNA | 0:75.54 1:0 | A:386600603;C:373317031;G:350339456;T:420938891;N:517200 | 75 | 0 | 386600603 | 373317031 | 350339456 | 420938891 | 517200 | ERX2160150 | ERS1883526 | ERA1011308 | Fundacao Champalimaud|European Nucleotide Archive | Fundacao Champalimaud|European Nucleotide Archive | 1 | 0.9552 | 0.08124 | 0.67685 | 0.47578 | 76 | B | usable mapping rate | illumina | early_illumina | unknown | random_priming | trueseq | bulk | unknown | unknown | Portugal | 2017-08-23 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||||||
| 9828 | 9828 | ERR2102838 | ERX2160149 | ERS1883525 | ERP040145 | PRJEB37796 | Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | E-MTAB-5992 | Transcriptome Analysis | We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals | ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992 | Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 | C3 control RNA | SAMEA104224507 | Fundacao Champalimaud | ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224507|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C3 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C3 control RNA|strain:AB | Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | E MTAB 5992:C3 control RNA s | C3 control RNA s | Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 | Experimental Factor: compound:PBS | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | ERP040145 | Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 | C3_R1_all.fastq.gz | fastq | 1380662008.0 | 18279108.0 | E MTAB 5992:C3 control RNA | 0:75.53 1:0 | A:345997031;C:338444594;G:316575258;T:379195977;N:449148 | 75 | 0 | 345997031 | 338444594 | 316575258 | 379195977 | 449148 | ERX2160149 | ERS1883525 | ERA1011308 | Fundacao Champalimaud|European Nucleotide Archive | Fundacao Champalimaud|European Nucleotide Archive | 1 | 0.95615 | 0.08131 | 0.68694 | 0.45267 | 74 | B | usable mapping rate | illumina | early_illumina | unknown | random_priming | trueseq | bulk | unknown | unknown | Portugal | 2017-08-23 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||||||
| 9829 | 9829 | ERR2102837 | ERX2160148 | ERS1883524 | ERP040145 | PRJEB37796 | Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | E-MTAB-5992 | Transcriptome Analysis | We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals | ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992 | Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 | C2 control RNA | SAMEA104224506 | Fundacao Champalimaud | ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224506|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C2 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C2 control RNA|strain:AB | Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | E MTAB 5992:C2 control RNA s | C2 control RNA s | Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 | Experimental Factor: compound:PBS | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | ERP040145 | Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 | C2_R1_all.fastq.gz | fastq | 1336640735.0 | 17695627.0 | E MTAB 5992:C2 control RNA | 0:75.54 1:0 | A:338213530;C:326808990;G:303983789;T:367147896;N:486530 | 75 | 0 | 338213530 | 326808990 | 303983789 | 367147896 | 486530 | ERX2160148 | ERS1883524 | ERA1011308 | Fundacao Champalimaud|European Nucleotide Archive | Fundacao Champalimaud|European Nucleotide Archive | 1 | 0.95427 | 0.08628 | 0.67706 | 0.47245 | 76 | B | usable mapping rate | illumina | early_illumina | unknown | random_priming | trueseq | bulk | unknown | unknown | Portugal | 2017-08-23 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||||||
| 9830 | 9830 | ERR2102836 | ERX2160147 | ERS1883523 | ERP040145 | PRJEB37796 | Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | E-MTAB-5992 | Transcriptome Analysis | We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals | ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992 | Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 | C1 control RNA | SAMEA104224505 | Fundacao Champalimaud | ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224505|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C1 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C1 control RNA|strain:AB | Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | E MTAB 5992:C1 control RNA s | C1 control RNA s | Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 | Experimental Factor: compound:PBS | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | ERP040145 | Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf | ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 | C1_R1_all.fastq.gz | fastq | 1297694845.0 | 17180544.0 | E MTAB 5992:C1 control RNA | 0:75.53 1:0 | A:322048172;C:316542683;G:299227724;T:359449433;N:426833 | 75 | 0 | 322048172 | 316542683 | 299227724 | 359449433 | 426833 | ERX2160147 | ERS1883523 | ERA1011308 | Fundacao Champalimaud|European Nucleotide Archive | Fundacao Champalimaud|European Nucleotide Archive | 1 | 0.95505 | 0.08541 | 0.67659 | 0.48159 | 75 | B | usable mapping rate | illumina | early_illumina | unknown | random_priming | trueseq | bulk | unknown | unknown | Portugal | 2017-08-23 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||||||
| 10141 | 10141 | ERR4973564 | ERX4792138 | ERS5459722 | ERP125703 | PRJEB41864 | three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E-MTAB-9899 | Transcriptome Analysis | mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced. | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10 | Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina | sibling 3 | SAMEA7703213 | Centre for Developmental Neurobiology King's College London | ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703213|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sibling 3|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 9899:sibling 3 | NextSeq 500 sequencing; 3 prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E MTAB 9899:sibling 3 s | sibling 3 s | three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina | Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | RACE | SINGLE | ILLUMINA | NextSeq 500 | ERP125703 | NextSeq 500 sequencing; three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10 | 70_AACCGA_70_ACTAGC_S2_R1_001.fastq.gz | fastq | E MTAB 9899:sibling 3 | 0:76 1:0 | A:385382600;C:210104151;G:238678838;T:315495923;N:5536 | 76 | 0 | 385382600 | 210104151 | 238678838 | 315495923 | 5536 | ERX4792138 | ERS5459722 | ERA3194022 | Centre for Developmental Neurobiology King | Centre for Developmental Neurobiology King | 1 | 0.82613 | 0.13111 | 0.77597 | 0.53833 | 76 | B | usable mapping rate | illumina | nextseq | 3prime | other | lexogen | bulk | unknown | unknown | United Kingdom | 2020-12-10 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||||||||
| 10142 | 10142 | ERR4973563 | ERX4792137 | ERS5459721 | ERP125703 | PRJEB41864 | three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E-MTAB-9899 | Transcriptome Analysis | mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced. | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10 | Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina | sibling 2 | SAMEA7703212 | Centre for Developmental Neurobiology King's College London | ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703212|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sibling 2|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 9899:sibling 2 | NextSeq 500 sequencing; 3 prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E MTAB 9899:sibling 2 s | sibling 2 s | three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina | Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | RACE | SINGLE | ILLUMINA | NextSeq 500 | ERP125703 | NextSeq 500 sequencing; three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10 | 69_AGTTGA_69_CTTACA_S7_R1_001.fastq.gz | fastq | E MTAB 9899:sibling 2 | 0:76 1:0 | A:405337161;C:226099266;G:255734601;T:341120121;N:5955 | 76 | 0 | 405337161 | 226099266 | 255734601 | 341120121 | 5955 | ERX4792137 | ERS5459721 | ERA3194022 | Centre for Developmental Neurobiology King | Centre for Developmental Neurobiology King | 1 | 0.84066 | 0.12241 | 0.77755 | 0.56472 | 76 | B | usable mapping rate | illumina | nextseq | 3prime | other | lexogen | bulk | unknown | unknown | United Kingdom | 2020-12-10 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||||||||
| 10143 | 10143 | ERR4973562 | ERX4792136 | ERS5459720 | ERP125703 | PRJEB41864 | three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E-MTAB-9899 | Transcriptome Analysis | mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced. | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10 | Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina | sibling 1 | SAMEA7703211 | Centre for Developmental Neurobiology King's College London | ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703211|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sibling 1|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 9899:sibling 1 | NextSeq 500 sequencing; 3 prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E MTAB 9899:sibling 1 s | sibling 1 s | three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina | Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | RACE | SINGLE | ILLUMINA | NextSeq 500 | ERP125703 | NextSeq 500 sequencing; three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10 | 68_CCAATT_68_GTCCCG_S11_R1_001.fastq.gz | fastq | E MTAB 9899:sibling 1 | 0:76 1:0 | A:440539801;C:236835299;G:268057277;T:355636994;N:6169 | 76 | 0 | 440539801 | 236835299 | 268057277 | 355636994 | 6169 | ERX4792136 | ERS5459720 | ERA3194022 | Centre for Developmental Neurobiology King | Centre for Developmental Neurobiology King | 1 | 0.82002 | 0.12908 | 0.77766 | 0.54981 | 76 | B | usable mapping rate | illumina | nextseq | 3prime | other | lexogen | bulk | unknown | unknown | United Kingdom | 2020-12-10 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||||||||
| 10144 | 10144 | ERR4973561 | ERX4792135 | ERS5459719 | ERP125703 | PRJEB41864 | three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E-MTAB-9899 | Transcriptome Analysis | mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced. | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10 | Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina | sfpq 3 | SAMEA7703210 | Centre for Developmental Neurobiology King's College London | ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703210|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sfpq 3|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:sfpq / |organism part:whole organism|sample name:E MTAB 9899:sfpq 3 | NextSeq 500 sequencing; 3 prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E MTAB 9899:sfpq 3 s | sfpq 3 s | three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina | Experimental Factor: genotype:sfpq / | RNA-Seq | TRANSCRIPTOMIC | RACE | SINGLE | ILLUMINA | NextSeq 500 | ERP125703 | NextSeq 500 sequencing; three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10 | 67_TCGTTC_67_TGCTAT_S22_R1_001.fastq.gz | fastq | E MTAB 9899:sfpq 3 | 0:76 1:0 | A:493165327;C:268347233;G:303443918;T:399152596;N:7138 | 76 | 0 | 493165327 | 268347233 | 303443918 | 399152596 | 7138 | ERX4792135 | ERS5459719 | ERA3194022 | Centre for Developmental Neurobiology King | Centre for Developmental Neurobiology King | 1 | 0.82521 | 0.12349 | 0.78545 | 0.57446 | 76 | B | usable mapping rate | illumina | nextseq | 3prime | other | lexogen | bulk | unknown | unknown | United Kingdom | 2020-12-10 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||||||||
| 10145 | 10145 | ERR4973560 | ERX4792134 | ERS5459718 | ERP125703 | PRJEB41864 | three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E-MTAB-9899 | Transcriptome Analysis | mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced. | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10 | Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina | sfpq 2 | SAMEA7703209 | Centre for Developmental Neurobiology King's College London | ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703209|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sfpq 2|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:sfpq / |organism part:whole organism|sample name:E MTAB 9899:sfpq 2 | NextSeq 500 sequencing; 3 prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E MTAB 9899:sfpq 2 s | sfpq 2 s | three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina | Experimental Factor: genotype:sfpq / | RNA-Seq | TRANSCRIPTOMIC | RACE | SINGLE | ILLUMINA | NextSeq 500 | ERP125703 | NextSeq 500 sequencing; three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10 | 66_GACGAT_66_TCAGTC_S18_R1_001.fastq.gz | fastq | E MTAB 9899:sfpq 2 | 0:76 1:0 | A:426637005;C:227027693;G:257342561;T:338159540;N:5909 | 76 | 0 | 426637005 | 227027693 | 257342561 | 338159540 | 5909 | ERX4792134 | ERS5459718 | ERA3194022 | Centre for Developmental Neurobiology King | Centre for Developmental Neurobiology King | 1 | 0.81933 | 0.11571 | 0.78593 | 0.56675 | 76 | B | usable mapping rate | illumina | nextseq | 3prime | other | lexogen | bulk | unknown | unknown | United Kingdom | 2020-12-10 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||||||||||||
| 10146 | 10146 | ERR4973559 | ERX4792133 | ERS5459717 | ERP125703 | PRJEB41864 | three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E-MTAB-9899 | Transcriptome Analysis | mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced. | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10 | Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina | sfpq 1 | SAMEA7703208 | Centre for Developmental Neurobiology King's College London | ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703208|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sfpq 1|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:sfpq / |organism part:whole organism|sample name:E MTAB 9899:sfpq 1 | NextSeq 500 sequencing; 3 prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E MTAB 9899:sfpq 1 s | sfpq 1 s | three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina | Experimental Factor: genotype:sfpq / | RNA-Seq | TRANSCRIPTOMIC | RACE | SINGLE | ILLUMINA | NextSeq 500 | ERP125703 | NextSeq 500 sequencing; three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10 | 65_AAGCTC_65_AAGAAG_S3_R1_001.fastq.gz | fastq | E MTAB 9899:sfpq 1 | 0:76 1:0 | A:425613638;C:225707961;G:254738302;T:336863560;N:5847 | 76 | 0 | 425613638 | 225707961 | 254738302 | 336863560 | 5847 | ERX4792133 | ERS5459717 | ERA3194022 | Centre for Developmental Neurobiology King | Centre for Developmental Neurobiology King | 1 | 0.81857 | 0.11342 | 0.78587 | 0.56439 | 76 | B | usable mapping rate | illumina | nextseq | 3prime | other | lexogen | bulk | unknown | unknown | United Kingdom | 2020-12-10 | Multi-stage | Multi-stage | 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 | ||||||||||||||||||||
| 11130 | 11130 | ERR9979395 | ERX9520370 | ERS12499848 | ERP139765 | PRJEB54901 | Single cell RNA sequencing of germ free zebrafish embryos | E-MTAB-11984 | Transcriptome Analysis | The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish. Here we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish. | ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22 | Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w… | Sample 2 WT GO+BA | SAMEA110401656 | Institute of Environmental Medicine, Karolinska Institutet | ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401656|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet|INSDC center name:Institute of Environmental Medicine Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 2 WT GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 2 WT GO+BA|sex:not available|stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM|strain:AB | Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos | E MTAB 11984:Sample 2 WT GO+BA p | Sample 2 WT GO+BA p | Single cell RNA sequencing of germ free zebrafish embryos | The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM with 10% FBS… | Experimental Factor: stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM | AMPLICON | TRANSCRIPTOMIC SINGLE CELL | size fractionation | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP139765 | Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos | ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22 | P22202_7002_S2_L002_R1_001.fastq.gz P22202_7002_S2_L002_R2_001.fastq.gz | fastq fastq | 18144406998.0 | 153766161.0 | E MTAB 11984:P22202 7002 S2 L002 | 0:28 1:90 | A:5277424121;C:3880928155;G:4118706097;T:4866649878;N:698747 | 28 | 90 | 5277424121 | 3880928155 | 4118706097 | 4866649878 | 698747 | ERX9520370 | ERS12499848 | ERA16483151 | Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive | Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive | 2 | 0.0109 | 0.90145 | 0.0053 | 0.21373 | 0.98746 | 0.79423 | 0.41198 | 0.54447 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | full_length | size_fractionation | trueseq | sc | single_cell_droplet | 10x | Sweden | 2022-07-22 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||
| 11131 | 11131 | ERR9979394 | ERX9520370 | ERS12499848 | ERP139765 | PRJEB54901 | Single cell RNA sequencing of germ free zebrafish embryos | E-MTAB-11984 | Transcriptome Analysis | The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish. Here we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish. | ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22 | Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w… | Sample 2 WT GO+BA | SAMEA110401656 | Institute of Environmental Medicine, Karolinska Institutet | ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401656|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet|INSDC center name:Institute of Environmental Medicine Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 2 WT GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 2 WT GO+BA|sex:not available|stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM|strain:AB | Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos | E MTAB 11984:Sample 2 WT GO+BA p | Sample 2 WT GO+BA p | Single cell RNA sequencing of germ free zebrafish embryos | The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM with 10% FBS… | Experimental Factor: stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM | AMPLICON | TRANSCRIPTOMIC SINGLE CELL | size fractionation | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP139765 | Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos | ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22 | P22202_7002_S2_L001_R1_001.fastq.gz P22202_7002_S2_L001_R2_001.fastq.gz | fastq fastq | 18458951574.0 | 156431793.0 | E MTAB 11984:P22202 7002 S2 L001 | 0:28 1:90 | A:5372920926;C:3946687814;G:4185647697;T:4953205454;N:489683 | 28 | 90 | 5372920926 | 3946687814 | 4185647697 | 4953205454 | 489683 | ERX9520370 | ERS12499848 | ERA16483151 | Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive | Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive | 2 | 0.01037 | 0.90168 | 0.0048 | 0.21246 | 0.98752 | 0.79297 | 0.42601 | 0.54996 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | full_length | size_fractionation | trueseq | sc | single_cell_droplet | 10x | Sweden | 2022-07-22 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||
| 11132 | 11132 | ERR9979392 | ERX9520369 | ERS12499847 | ERP139765 | PRJEB54901 | Single cell RNA sequencing of germ free zebrafish embryos | E-MTAB-11984 | Transcriptome Analysis | The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish. Here we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish. | ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22 | Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w… | Sample 1 WT control | SAMEA110401655 | Institute of Environmental Medicine, Karolinska Institutet | ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401655|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet|INSDC center name:Institute of Environmental Medicine Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 1 WT control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 1 WT control|sex:not available|stimulus:n1|strain:AB | Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos | E MTAB 11984:Sample 1 WT control p | Sample 1 WT control p | Single cell RNA sequencing of germ free zebrafish embryos | The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM with 10% FBS… | Experimental Factor: stimulus:n1 | AMPLICON | TRANSCRIPTOMIC SINGLE CELL | size fractionation | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP139765 | Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos | ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22 | P22202_7001_S1_L001_R1_001.fastq.gz P22202_7001_S1_L001_R2_001.fastq.gz | fastq fastq | 19396994226.0 | 164381307.0 | E MTAB 11984:P22202 7001 S1 L001 | 0:28 1:90 | A:5665199484;C:4091196594;G:4415211076;T:5224866754;N:520318 | 28 | 90 | 5665199484 | 4091196594 | 4415211076 | 5224866754 | 520318 | ERX9520369 | ERS12499847 | ERA16483151 | Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive | Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive | 2 | 0.01093 | 0.89238 | 0.00557 | 0.232 | 0.98764 | 0.79444 | 0.40806 | 0.54781 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | full_length | size_fractionation | trueseq | sc | single_cell_droplet | 10x | Sweden | 2022-07-22 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||
| 11133 | 11133 | ERR9979393 | ERX9520369 | ERS12499847 | ERP139765 | PRJEB54901 | Single cell RNA sequencing of germ free zebrafish embryos | E-MTAB-11984 | Transcriptome Analysis | The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish. Here we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish. | ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22 | Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w… | Sample 1 WT control | SAMEA110401655 | Institute of Environmental Medicine, Karolinska Institutet | ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401655|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet|INSDC center name:Institute of Environmental Medicine Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 1 WT control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 1 WT control|sex:not available|stimulus:n1|strain:AB | Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos | E MTAB 11984:Sample 1 WT control p | Sample 1 WT control p | Single cell RNA sequencing of germ free zebrafish embryos | The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM with 10% FBS… | Experimental Factor: stimulus:n1 | AMPLICON | TRANSCRIPTOMIC SINGLE CELL | size fractionation | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP139765 | Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos | ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22 | P22202_7001_S1_L002_R1_001.fastq.gz P22202_7001_S1_L002_R2_001.fastq.gz | fastq fastq | 19063958224.0 | 161558968.0 | E MTAB 11984:P22202 7001 S1 L002 | 0:28 1:90 | A:5563588848;C:4022930643;G:4344549562;T:5132136743;N:752428 | 28 | 90 | 5563588848 | 4022930643 | 4344549562 | 5132136743 | 752428 | ERX9520369 | ERS12499847 | ERA16483151 | Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive | Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive | 2 | 0.01118 | 0.89308 | 0.00573 | 0.23128 | 0.98737 | 0.79354 | 0.39264 | 0.54552 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | full_length | size_fractionation | trueseq | sc | single_cell_droplet | 10x | Sweden | 2022-07-22 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||
| 11238 | 11238 | ERR10782555 | ERX10233132 | ERS14439197 | ERP144048 | PRJEB58983 | RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling | E-MTAB-12503 | Transcriptome Analysis | Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… | ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 | Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. | Sample 6 | E MTAB 12503:Sample 6 | strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 6|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 | Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling | E MTAB 12503:Sample 6 p | Sample 6 p | RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling | Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. | Experimental Factor: developmental stage:bud|Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | RANDOM | PAIRED | ILLUMINA | Illumina HiSeq 4000 | ERP144048 | Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling | ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 | 20170530.A-6_R1.fastq.gz 20170530.A-6_R2.fastq.gz | fastq fastq | 14809693138.0 | 49038719.0 | E MTAB 12503:20170530.A 6 R | 0:151 1:151 | A:4069749497;C:3367864217;G:3430269434;T:3928390721;N:13419269 | 151 | 151 | 4069749497 | 3367864217 | 3430269434 | 3928390721 | 13419269 | ERX10233132 | ERS14439197 | ERA20162442 | University of Zurich|European Nucleotide Archive | University of Zurich|European Nucleotide Archive | 2 | 0.83945 | 0.69977 | 0.27269 | 0.22488 | 0.74523 | 0.77654 | 0.4899 | 0.4358 | 151 | 151 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | random_priming | trueseq | sc | unknown | unknown | Switzerland | 2023-03-31 | Multi-stage | Embryo | Whole Organism | All anatomical structures | ||||||||||||||
| 11239 | 11239 | ERR10782554 | ERX10233131 | ERS14439196 | ERP144048 | PRJEB58983 | RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling | E-MTAB-12503 | Transcriptome Analysis | Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… | ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 | Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. | Sample 5 | E MTAB 12503:Sample 5 | strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 5|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 | Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling | E MTAB 12503:Sample 5 p | Sample 5 p | RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling | Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. | Experimental Factor: developmental stage:bud|Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | RANDOM | PAIRED | ILLUMINA | Illumina HiSeq 4000 | ERP144048 | Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling | ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 | 20170530.A-5_R1.fastq.gz 20170530.A-5_R2.fastq.gz | fastq fastq | 14954968728.0 | 49519764.0 | E MTAB 12503:20170530.A 5 R | 0:151 1:151 | A:4063340262;C:3440933120;G:3455723079;T:3981396987;N:13575280 | 151 | 151 | 4063340262 | 3440933120 | 3455723079 | 3981396987 | 13575280 | ERX10233131 | ERS14439196 | ERA20162442 | University of Zurich|European Nucleotide Archive | University of Zurich|European Nucleotide Archive | 2 | 0.85891 | 0.86859 | 0.28842 | 0.28866 | 0.7349 | 0.75051 | 0.45532 | 0.49145 | 151 | 151 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | random_priming | trueseq | sc | unknown | unknown | Switzerland | 2023-03-31 | Multi-stage | Embryo | Whole Organism | All anatomical structures | ||||||||||||||
| 11242 | 11242 | ERR10782551 | ERX10233128 | ERS14439193 | ERP144048 | PRJEB58983 | RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling | E-MTAB-12503 | Transcriptome Analysis | Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… | ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 | Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. | Sample 7 | E MTAB 12503:Sample 7 | strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 7|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 | Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling | E MTAB 12503:Sample 7 p | Sample 7 p | RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling | Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. | Experimental Factor: developmental stage:bud|Experimental Factor: genotype:rbm8a d5/d5 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | RANDOM | PAIRED | ILLUMINA | Illumina HiSeq 4000 | ERP144048 | Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling | ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 | 20170530.A-7_R1.fastq.gz 20170530.A-7_R2.fastq.gz | fastq fastq | 12726557236.0 | 42140918.0 | E MTAB 12503:20170530.A 7 R | 0:151 1:151 | A:3510176970;C:2879679978;G:2932244172;T:3392911734;N:11544382 | 151 | 151 | 3510176970 | 2879679978 | 2932244172 | 3392911734 | 11544382 | ERX10233128 | ERS14439193 | ERA20162442 | University of Zurich|European Nucleotide Archive | University of Zurich|European Nucleotide Archive | 2 | 0.88531 | 0.88678 | 0.33279 | 0.3329 | 0.73545 | 0.74992 | 0.52548 | 0.52864 | 151 | 151 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | random_priming | trueseq | sc | unknown | unknown | Switzerland | 2023-03-31 | Multi-stage | Embryo | Whole Organism | All anatomical structures | ||||||||||||||
| 11821 | 11821 | ERR11834690 | ERX11232843 | ERS16254762 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 4 | SAMEA114265804 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265804|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 4|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250|organism part:whole organism|rin:9.6|sample name:E MTAB 13263:Sample 4|scientific name:Danio rerio|sex:na|stimulus:immunosuppression|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 4 p | Sample 4 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2113_dre_C1_clobetasolpropionate_lib667285_10169_3_2.fastq.gz NG-32417_R2113_dre_C1_clobetasolpropionate_lib667285_10169_3_1.fastq.gz | fastq fastq | 9764006696.0 | 32331148.0 | E MTAB 13263:NG 32417 R2113 dre C1 clobetasolpropionate lib667285 10169 3 | 0:151 1:151 | A:2627275848;C:2223323771;G:2323190525;T:2590103027;N:113525 | 151 | 151 | 2627275848 | 2223323771 | 2323190525 | 2590103027 | 113525 | ERX11232843 | ERS16254762 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.95424 | 0.95502 | 0.12596 | 0.12401 | 0.65884 | 0.65825 | 0.48134 | 0.48327 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11822 | 11822 | ERR11834689 | ERX11232842 | ERS16254761 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 3 | SAMEA114265803 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265803|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 3|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:0|organism part:whole organism|rin:9.4|sample name:E MTAB 13263:Sample 3|scientific name:Danio rerio|sex:na|stimulus:n1|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 3 p | Sample 3 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2112_dre_nc_clobetasolpropionate_lib673071_10180_1_2.fastq.gz NG-32417_R2112_dre_nc_clobetasolpropionate_lib673071_10180_1_1.fastq.gz | fastq fastq | 13326663550.0 | 44128025.0 | E MTAB 13263:NG 32417 R2112 dre nc clobetasolpropionate lib673071 10180 1 | 0:151 1:151 | A:3641640344;C:3020489123;G:3072643196;T:3591659412;N:231475 | 151 | 151 | 3641640344 | 3020489123 | 3072643196 | 3591659412 | 231475 | ERX11232842 | ERS16254761 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.95271 | 0.95293 | 0.11945 | 0.1151 | 0.65819 | 0.6579 | 0.47257 | 0.47803 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11823 | 11823 | ERR11834684 | ERX11232837 | ERS16254756 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 1 | SAMEA114265798 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265798|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 1|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:0|organism part:whole organism|rin:9.3|sample name:E MTAB 13263:Sample 1|scientific name:Danio rerio|sex:na|stimulus:n1|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 1 p | Sample 1 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2110_dre_nc_clobetasolpropionate_lib667282_10169_3_1.fastq.gz NG-32417_R2110_dre_nc_clobetasolpropionate_lib667282_10169_3_2.fastq.gz | fastq fastq | 10152616370.0 | 33617935.0 | E MTAB 13263:NG 32417 R2110 dre nc clobetasolpropionate lib667282 10169 3 | 0:151 1:151 | A:2743478864;C:2319134955;G:2378048842;T:2711839167;N:114542 | 151 | 151 | 2743478864 | 2319134955 | 2378048842 | 2711839167 | 114542 | ERX11232837 | ERS16254756 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.95273 | 0.95457 | 0.13567 | 0.13174 | 0.65896 | 0.65841 | 0.47947 | 0.47815 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11824 | 11824 | ERR11834691 | ERX11232844 | ERS16254763 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 5 | SAMEA114265805 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265805|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 5|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250|organism part:whole organism|rin:9.2|sample name:E MTAB 13263:Sample 5|scientific name:Danio rerio|sex:na|stimulus:immunosuppression|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 5 p | Sample 5 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2114_dre_C1_clobetasolpropionate_lib667286_10169_3_1.fastq.gz NG-32417_R2114_dre_C1_clobetasolpropionate_lib667286_10169_3_2.fastq.gz | fastq fastq | 11690304334.0 | 38709617.0 | E MTAB 13263:NG 32417 R2114 dre C1 clobetasolpropionate lib667286 10169 3 | 0:151 1:151 | A:3142106866;C:2677986743;G:2767050957;T:3103028799;N:130969 | 151 | 151 | 3142106866 | 2677986743 | 2767050957 | 3103028799 | 130969 | ERX11232844 | ERS16254763 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.95418 | 0.95523 | 0.12548 | 0.12397 | 0.66026 | 0.66016 | 0.46767 | 0.47253 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11825 | 11825 | ERR11834688 | ERX11232841 | ERS16254760 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 2 | SAMEA114265802 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265802|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 2|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:0|organism part:whole organism|rin:9.6|sample name:E MTAB 13263:Sample 2|scientific name:Danio rerio|sex:na|stimulus:n1|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 2 p | Sample 2 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2111_dre_nc_clobetasolpropionate_lib673070_10180_1_1.fastq.gz NG-32417_R2111_dre_nc_clobetasolpropionate_lib673070_10180_1_2.fastq.gz | fastq fastq | 11827163184.0 | 39162792.0 | E MTAB 13263:NG 32417 R2111 dre nc clobetasolpropionate lib673070 10180 1 | 0:151 1:151 | A:3256286612;C:2657918302;G:2701905502;T:3210846546;N:206222 | 151 | 151 | 3256286612 | 2657918302 | 2701905502 | 3210846546 | 206222 | ERX11232841 | ERS16254760 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.95203 | 0.95292 | 0.12277 | 0.11772 | 0.66048 | 0.65837 | 0.47243 | 0.4729 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11826 | 11826 | ERR11834693 | ERX11232846 | ERS16254765 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 7 | SAMEA114265807 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265807|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 7|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:4000|organism part:whole organism|rin:9.7|sample name:E MTAB 13263:Sample 7|scientific name:Danio rerio|sex:na|stimulus:immunostimulation|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 7 p | Sample 7 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2116_dre_nc_imq_clobetasolpropionate_lib667288_10169_3_1.fastq.gz NG-32417_R2116_dre_nc_imq_clobetasolpropionate_lib667288_10169_3_2.fastq.gz | fastq fastq | 11114382784.0 | 36802592.0 | E MTAB 13263:NG 32417 R2116 dre nc imq clobetasolpropionate lib667288 10169 3 | 0:151 1:151 | A:2997376944;C:2547742011;G:2613273908;T:2955864850;N:125071 | 151 | 151 | 2997376944 | 2547742011 | 2613273908 | 2955864850 | 125071 | ERX11232846 | ERS16254765 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.95392 | 0.9539 | 0.12951 | 0.12707 | 0.65628 | 0.65731 | 0.48132 | 0.48179 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11827 | 11827 | ERR11834695 | ERX11232848 | ERS16254767 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 9 | SAMEA114265809 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265809|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 9|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:4000|organism part:whole organism|rin:9.9|sample name:E MTAB 13263:Sample 9|scientific name:Danio rerio|sex:na|stimulus:immunostimulation|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 9 p | Sample 9 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2118_dre_nc_imq_clobetasolpropionate_lib667290_10169_3_1.fastq.gz NG-32417_R2118_dre_nc_imq_clobetasolpropionate_lib667290_10169_3_2.fastq.gz | fastq fastq | 9422294300.0 | 31199650.0 | E MTAB 13263:NG 32417 R2118 dre nc imq clobetasolpropionate lib667290 10169 3 | 0:151 1:151 | A:2541445212;C:2157798531;G:2214381344;T:2508560588;N:108625 | 151 | 151 | 2541445212 | 2157798531 | 2214381344 | 2508560588 | 108625 | ERX11232848 | ERS16254767 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.95337 | 0.95433 | 0.13046 | 0.12718 | 0.65845 | 0.65815 | 0.48198 | 0.48414 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11828 | 11828 | ERR11834687 | ERX11232840 | ERS16254759 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 12 | SAMEA114265801 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265801|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 12|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250 CP + 4000 IMQ|organism part:whole organism|rin:9.7|sample name:E MTAB 13263:Sample 12|scientific name:Danio rerio|sex:na|stimulus:immunosuppression and immunostimulation|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 12 p | Sample 12 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2121_dre_C1_imq_clobetasolpropionate_lib667293_10169_3_2.fastq.gz NG-32417_R2121_dre_C1_imq_clobetasolpropionate_lib667293_10169_3_1.fastq.gz | fastq fastq | 9285032280.0 | 30745140.0 | E MTAB 13263:NG 32417 R2121 dre C1 imq clobetasolpropionate lib667293 10169 3 | 0:151 1:151 | A:2504765552;C:2110325477;G:2196928032;T:2472905759;N:107460 | 151 | 151 | 2504765552 | 2110325477 | 2196928032 | 2472905759 | 107460 | ERX11232840 | ERS16254759 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.95411 | 0.95451 | 0.12502 | 0.12228 | 0.65829 | 0.65774 | 0.48259 | 0.47946 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11829 | 11829 | ERR11834694 | ERX11232847 | ERS16254766 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 8 | SAMEA114265808 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265808|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 8|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:4000|organism part:whole organism|rin:9.5|sample name:E MTAB 13263:Sample 8|scientific name:Danio rerio|sex:na|stimulus:immunostimulation|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 8 p | Sample 8 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2117_dre_nc_imq_clobetasolpropionate_lib667289_10169_3_1.fastq.gz NG-32417_R2117_dre_nc_imq_clobetasolpropionate_lib667289_10169_3_2.fastq.gz | fastq fastq | 10247527118.0 | 33932209.0 | E MTAB 13263:NG 32417 R2117 dre nc imq clobetasolpropionate lib667289 10169 3 | 0:151 1:151 | A:2766675319;C:2342307825;G:2405294253;T:2733131648;N:118073 | 151 | 151 | 2766675319 | 2342307825 | 2405294253 | 2733131648 | 118073 | ERX11232847 | ERS16254766 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.9541 | 0.95434 | 0.13364 | 0.13098 | 0.6576 | 0.6565 | 0.48068 | 0.48029 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11830 | 11830 | ERR11834692 | ERX11232845 | ERS16254764 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 6 | SAMEA114265806 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265806|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 6|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250|organism part:whole organism|rin:10|sample name:E MTAB 13263:Sample 6|scientific name:Danio rerio|sex:na|stimulus:immunosuppression|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 6 p | Sample 6 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2115_dre_C1_clobetasolpropionate_lib667287_10169_3_1.fastq.gz NG-32417_R2115_dre_C1_clobetasolpropionate_lib667287_10169_3_2.fastq.gz | fastq fastq | 10440673634.0 | 34571767.0 | E MTAB 13263:NG 32417 R2115 dre C1 clobetasolpropionate lib667287 10169 3 | 0:151 1:151 | A:2805459166;C:2397120759;G:2463616298;T:2774359989;N:117422 | 151 | 151 | 2805459166 | 2397120759 | 2463616298 | 2774359989 | 117422 | ERX11232845 | ERS16254764 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.95568 | 0.9548 | 0.13056 | 0.12563 | 0.65882 | 0.66332 | 0.49162 | 0.48586 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11831 | 11831 | ERR11834685 | ERX11232838 | ERS16254757 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 10 | SAMEA114265799 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265799|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 10|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250 CP + 4000 IMQ|organism part:whole organism|rin:9.4|sample name:E MTAB 13263:Sample 10|scientific name:Danio rerio|sex:na|stimulus:immunosuppression and immunostimulation|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 10 p | Sample 10 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2119_dre_C1_imq_clobetasolpropionate_lib667291_10169_3_2.fastq.gz NG-32417_R2119_dre_C1_imq_clobetasolpropionate_lib667291_10169_3_1.fastq.gz | fastq fastq | 11267068246.0 | 37308173.0 | E MTAB 13263:NG 32417 R2119 dre C1 imq clobetasolpropionate lib667291 10169 3 | 0:151 1:151 | A:3042432765;C:2574394239;G:2642086000;T:3008026288;N:128954 | 151 | 151 | 3042432765 | 2574394239 | 2642086000 | 3008026288 | 128954 | ERX11232838 | ERS16254757 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.95345 | 0.95411 | 0.13324 | 0.13062 | 0.65796 | 0.65892 | 0.48176 | 0.48174 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11832 | 11832 | ERR11834686 | ERX11232839 | ERS16254758 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 11 | SAMEA114265800 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265800|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 11|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250 CP + 4000 IMQ|organism part:whole organism|rin:10|sample name:E MTAB 13263:Sample 11|scientific name:Danio rerio|sex:na|stimulus:immunosuppression and immunostimulation|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 11 p | Sample 11 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2120_dre_C1_imq_clobetasolpropionate_lib667292_10169_3_2.fastq.gz NG-32417_R2120_dre_C1_imq_clobetasolpropionate_lib667292_10169_3_1.fastq.gz | fastq fastq | 9922486330.0 | 32855915.0 | E MTAB 13263:NG 32417 R2120 dre C1 imq clobetasolpropionate lib667292 10169 3 | 0:151 1:151 | A:2673462020;C:2268840894;G:2345658284;T:2634411815;N:113317 | 151 | 151 | 2673462020 | 2268840894 | 2345658284 | 2634411815 | 113317 | ERX11232839 | ERS16254758 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.9551 | 0.95621 | 0.1193 | 0.11675 | 0.65833 | 0.65827 | 0.48596 | 0.48547 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 13299 | 13299 | ERR984502 | ERX1065723 | ERS715232 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367580 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:55Z|ENA LAST UPDATE:2018 03 09T00:40:24Z|External Id:SAMEA3367580|INSDC center name:SC|INSDC first public:2015 08 18T09:04:55Z|INSDC last update:2018 03 09T00:40:24Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 24 sc 2286404|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo wild type for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TTCAGCTC is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 24 sc 2286404|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#24 | 13741631 | Illumina sequencing of library 13741631 constructed from sample accession ERS715232 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TTCAGCTC. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#24.cram | cram | 570705070.0 | 4390039.0 | SC RUN 16164 8#24 | 0:55 1:75 | A:167603013;C:88769000;G:138595187;T:175336986;N:400884 | 55 | 75 | 167603013 | 88769000 | 138595187 | 175336986 | 400884 | ERX1065723 | ERS715232 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.18131 | 0.44012 | 0.12372 | 0.1122 | 0.96759 | 0.93835 | 0.63426 | 0.57651 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13300 | 13300 | ERR984501 | ERX1065722 | ERS715231 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367579 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:55Z|ENA LAST UPDATE:2018 03 09T00:01:26Z|External Id:SAMEA3367579|INSDC center name:SC|INSDC first public:2015 08 18T09:04:55Z|INSDC last update:2018 03 09T00:01:26Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 23 sc 2286403|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo wild type for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TACTAGTC is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 23 sc 2286403|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#23 | 13741630 | Illumina sequencing of library 13741630 constructed from sample accession ERS715231 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TACTAGTC. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#23.cram | cram | 682831890.0 | 5252553.0 | SC RUN 16164 8#23 | 0:55 1:75 | A:201267036;C:106752351;G:152982998;T:221347859;N:481646 | 55 | 75 | 201267036 | 106752351 | 152982998 | 221347859 | 481646 | ERX1065722 | ERS715231 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.19992 | 0.5315 | 0.13001 | 0.13817 | 0.96025 | 0.92261 | 0.60527 | 0.55787 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13301 | 13301 | ERR984500 | ERX1065721 | ERS715230 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367578 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:01:26Z|External Id:SAMEA3367578|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:01:26Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 22 sc 2286402|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo wild type for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TCAGATTC is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 22 sc 2286402|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#22 | 13741629 | Illumina sequencing of library 13741629 constructed from sample accession ERS715230 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TCAGATTC. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#22.cram | cram | 822730220.0 | 6328694.0 | SC RUN 16164 8#22 | 0:55 1:75 | A:241693794;C:130571512;G:177853465;T:272028770;N:582679 | 55 | 75 | 241693794 | 130571512 | 177853465 | 272028770 | 582679 | ERX1065721 | ERS715230 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.2212 | 0.54203 | 0.15635 | 0.13659 | 0.96159 | 0.9221 | 0.59031 | 0.55109 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13302 | 13302 | ERR984499 | ERX1065720 | ERS715229 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367577 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:40:24Z|External Id:SAMEA3367577|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:40:24Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 21 sc 2286401|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo wild type for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TATGCCAG is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 21 sc 2286401|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#21 | 13741628 | Illumina sequencing of library 13741628 constructed from sample accession ERS715229 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TATGCCAG. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#21.cram | cram | 616663190.0 | 4743563.0 | SC RUN 16164 8#21 | 0:55 1:75 | A:176848806;C:99629161;G:137029831;T:202730142;N:425250 | 55 | 75 | 176848806 | 99629161 | 137029831 | 202730142 | 425250 | ERX1065720 | ERS715229 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.21864 | 0.57174 | 0.1516 | 0.14103 | 0.95905 | 0.9192 | 0.55513 | 0.51633 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13303 | 13303 | ERR984498 | ERX1065719 | ERS715228 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367576 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:01:26Z|External Id:SAMEA3367576|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:01:26Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 20 sc 2286400|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo wild type for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TGGCTCAG is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 20 sc 2286400|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#20 | 13741627 | Illumina sequencing of library 13741627 constructed from sample accession ERS715228 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TGGCTCAG. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#20.cram | cram | 708059950.0 | 5446615.0 | SC RUN 16164 8#20 | 0:55 1:75 | A:195264246;C:129715499;G:160155422;T:222438911;N:485872 | 55 | 75 | 195264246 | 129715499 | 160155422 | 222438911 | 485872 | ERX1065719 | ERS715228 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.19642 | 0.48584 | 0.11921 | 0.11811 | 0.95422 | 0.91843 | 0.62494 | 0.56646 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13304 | 13304 | ERR984497 | ERX1065718 | ERS715227 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367575 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:01:26Z|External Id:SAMEA3367575|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:01:26Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 19 sc 2286399|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo wild type for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TCATTGAG is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 19 sc 2286399|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#19 | 13741626 | Illumina sequencing of library 13741626 constructed from sample accession ERS715227 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TCATTGAG. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#19.cram | cram | 651943890.0 | 5014953.0 | SC RUN 16164 8#19 | 0:55 1:75 | A:191809575;C:111573276;G:144109125;T:204007845;N:444069 | 55 | 75 | 191809575 | 111573276 | 144109125 | 204007845 | 444069 | ERX1065718 | ERS715227 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.17909 | 0.44616 | 0.12326 | 0.12424 | 0.96256 | 0.93432 | 0.56606 | 0.52819 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13305 | 13305 | ERR984496 | ERX1065717 | ERS715226 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367574 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:40:24Z|External Id:SAMEA3367574|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:40:24Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 18 sc 2286398|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo heterozygous for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TGTATGCG is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 18 sc 2286398|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#18 | 13741625 | Illumina sequencing of library 13741625 constructed from sample accession ERS715226 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TGTATGCG. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#18.cram | cram | 610476620.0 | 4695974.0 | SC RUN 16164 8#18 | 0:55 1:75 | A:181332724;C:99472616;G:132687929;T:196571397;N:411954 | 55 | 75 | 181332724 | 99472616 | 132687929 | 196571397 | 411954 | ERX1065717 | ERS715226 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.22636 | 0.55559 | 0.16123 | 0.16819 | 0.96025 | 0.92967 | 0.59576 | 0.54685 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13306 | 13306 | ERR984495 | ERX1065716 | ERS715225 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367573 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:01:26Z|External Id:SAMEA3367573|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:01:26Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 17 sc 2286397|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo heterozygous for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TCCAGTCG is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 17 sc 2286397|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#17 | 13741624 | Illumina sequencing of library 13741624 constructed from sample accession ERS715225 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TCCAGTCG. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#17.cram | cram | 712320830.0 | 5479391.0 | SC RUN 16164 8#17 | 0:55 1:75 | A:204316194;C:115198795;G:158608369;T:233717227;N:480245 | 55 | 75 | 204316194 | 115198795 | 158608369 | 233717227 | 480245 | ERX1065716 | ERS715225 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.2492 | 0.59739 | 0.17155 | 0.14862 | 0.95657 | 0.92056 | 0.58039 | 0.53475 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13307 | 13307 | ERR984494 | ERX1065715 | ERS715224 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367572 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:01:26Z|External Id:SAMEA3367572|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:01:26Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 16 sc 2286396|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo heterozygous for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TAAGTTCG is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 16 sc 2286396|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#16 | 13741623 | Illumina sequencing of library 13741623 constructed from sample accession ERS715224 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TAAGTTCG. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#16.cram | cram | 793769340.0 | 6105918.0 | SC RUN 16164 8#16 | 0:55 1:75 | A:232264866;C:130235228;G:171709756;T:259013732;N:545758 | 55 | 75 | 232264866 | 130235228 | 171709756 | 259013732 | 545758 | ERX1065715 | ERS715224 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.22065 | 0.5061 | 0.15274 | 0.13242 | 0.95779 | 0.92575 | 0.57619 | 0.53869 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13308 | 13308 | ERR984493 | ERX1065714 | ERS715223 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367571 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:40:24Z|External Id:SAMEA3367571|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:40:24Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 15 sc 2286395|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo heterozygous for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TCAGGAGG is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 15 sc 2286395|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#15 | 13741622 | Illumina sequencing of library 13741622 constructed from sample accession ERS715223 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TCAGGAGG. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#15.cram | cram | 785479760.0 | 6042152.0 | SC RUN 16164 8#15 | 0:55 1:75 | A:221631721;C:150326010;G:172964474;T:240036379;N:521176 | 55 | 75 | 221631721 | 150326010 | 172964474 | 240036379 | 521176 | ERX1065714 | ERS715223 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.26761 | 0.37751 | 0.19858 | 0.09301 | 0.95162 | 0.93129 | 0.56282 | 0.54289 | 55 | 75 | B | B | mate1-mate2 similar by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13309 | 13309 | ERR984492 | ERX1065713 | ERS715222 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367570 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:01:26Z|External Id:SAMEA3367570|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:01:26Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 14 sc 2286394|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo heterozygous for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TCTCACGG is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 14 sc 2286394|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#14 | 13741621 | Illumina sequencing of library 13741621 constructed from sample accession ERS715222 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TCTCACGG. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#14.cram | cram | 673293530.0 | 5179181.0 | SC RUN 16164 8#14 | 0:55 1:75 | A:188203068;C:115934699;G:155324541;T:213374769;N:456453 | 55 | 75 | 188203068 | 115934699 | 155324541 | 213374769 | 456453 | ERX1065713 | ERS715222 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.21855 | 0.57586 | 0.15197 | 0.14501 | 0.95946 | 0.93077 | 0.56453 | 0.52351 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13310 | 13310 | ERR984491 | ERX1065712 | ERS715221 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367569 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:01:26Z|External Id:SAMEA3367569|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:01:26Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 13 sc 2286393|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo heterozygous for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TACTTCGG is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 13 sc 2286393|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#13 | 13741620 | Illumina sequencing of library 13741620 constructed from sample accession ERS715221 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TACTTCGG. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#13.cram | cram | 783634020.0 | 6027954.0 | SC RUN 16164 8#13 | 0:55 1:75 | A:231435775;C:129417634;G:178939153;T:243302897;N:538561 | 55 | 75 | 231435775 | 129417634 | 178939153 | 243302897 | 538561 | ERX1065712 | ERS715221 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.20287 | 0.52947 | 0.14655 | 0.13479 | 0.96299 | 0.93703 | 0.56376 | 0.52626 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13311 | 13311 | ERR984490 | ERX1065711 | ERS715220 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367568 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:40:24Z|External Id:SAMEA3367568|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:40:24Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 12 sc 2286392|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo homozygous for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TGAACTGG is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 12 sc 2286392|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#12 | 13741619 | Illumina sequencing of library 13741619 constructed from sample accession ERS715220 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TGAACTGG. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#12.cram | cram | 746397730.0 | 5741521.0 | SC RUN 16164 8#12 | 0:55 1:75 | A:217959769;C:123138989;G:158254272;T:246531930;N:512770 | 55 | 75 | 217959769 | 123138989 | 158254272 | 246531930 | 512770 | ERX1065711 | ERS715220 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.20695 | 0.57674 | 0.14123 | 0.14978 | 0.95899 | 0.9138 | 0.56705 | 0.57522 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13312 | 13312 | ERR984489 | ERX1065710 | ERS715219 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367567 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:55Z|ENA LAST UPDATE:2018 03 09T00:01:26Z|External Id:SAMEA3367567|INSDC center name:SC|INSDC first public:2015 08 18T09:04:55Z|INSDC last update:2018 03 09T00:01:26Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 11 sc 2286391|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo homozygous for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TTGGTATG is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 11 sc 2286391|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#11 | 13741618 | Illumina sequencing of library 13741618 constructed from sample accession ERS715219 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TTGGTATG. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#11.cram | cram | 630077890.0 | 4846753.0 | SC RUN 16164 8#11 | 0:55 1:75 | A:181555459;C:107913967;G:131155798;T:209016157;N:436509 | 55 | 75 | 181555459 | 107913967 | 131155798 | 209016157 | 436509 | ERX1065710 | ERS715219 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.23034 | 0.58664 | 0.14994 | 0.16031 | 0.9517 | 0.9134 | 0.43491 | 0.55537 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13313 | 13313 | ERR984488 | ERX1065709 | ERS715218 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367566 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:57Z|ENA LAST UPDATE:2018 03 09T00:00:47Z|External Id:SAMEA3367566|INSDC center name:SC|INSDC first public:2015 08 18T09:04:57Z|INSDC last update:2018 03 09T00:00:47Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 10 sc 2286390|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo homozygous for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TAACGCTG is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 10 sc 2286390|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#10 | 13741617 | Illumina sequencing of library 13741617 constructed from sample accession ERS715218 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TAACGCTG. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#10.cram | cram | 522425410.0 | 4018657.0 | SC RUN 16164 8#10 | 0:55 1:75 | A:136789388;C:88820863;G:131305976;T:165156817;N:352366 | 55 | 75 | 136789388 | 88820863 | 131305976 | 165156817 | 352366 | ERX1065709 | ERS715218 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.16976 | 0.61187 | 0.10677 | 0.16777 | 0.96096 | 0.93093 | 0.59603 | 0.58893 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13314 | 13314 | ERR984487 | ERX1065708 | ERS715217 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367565 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:40:24Z|External Id:SAMEA3367565|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:40:24Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 9 sc 2286389|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo homozygous for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TCGAAGTG is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 9 sc 2286389|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#9 | 13741616 | Illumina sequencing of library 13741616 constructed from sample accession ERS715217 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TCGAAGTG. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#9.cram | cram | 662372100.0 | 5095170.0 | SC RUN 16164 8#9 | 0:55 1:75 | A:186346528;C:114321445;G:137139385;T:224106023;N:458719 | 55 | 75 | 186346528 | 114321445 | 137139385 | 224106023 | 458719 | ERX1065708 | ERS715217 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.22854 | 0.63729 | 0.14734 | 0.16003 | 0.95089 | 0.90751 | 0.51773 | 0.50977 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13315 | 13315 | ERR984486 | ERX1065707 | ERS715216 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367564 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:55Z|ENA LAST UPDATE:2018 03 09T00:00:47Z|External Id:SAMEA3367564|INSDC center name:SC|INSDC first public:2015 08 18T09:04:55Z|INSDC last update:2018 03 09T00:00:47Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 8 sc 2286388|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo homozygous for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TTCCATTG is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 8 sc 2286388|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#8 | 13741615 | Illumina sequencing of library 13741615 constructed from sample accession ERS715216 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TTCCATTG. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#8.cram | cram | 857007060.0 | 6592362.0 | SC RUN 16164 8#8 | 0:55 1:75 | A:257958701;C:131661477;G:190276240;T:276500331;N:610311 | 55 | 75 | 257958701 | 131661477 | 190276240 | 276500331 | 610311 | ERX1065707 | ERS715216 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.21266 | 0.595 | 0.14225 | 0.14037 | 0.95964 | 0.92232 | 0.54595 | 0.53111 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13316 | 13316 | ERR984485 | ERX1065706 | ERS715215 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367563 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:00:47Z|External Id:SAMEA3367563|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:00:47Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 7 sc 2286387|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo homozygous for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TAGTCTTG is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 7 sc 2286387|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#7 | 13741614 | Illumina sequencing of library 13741614 constructed from sample accession ERS715215 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TAGTCTTG. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#7.cram | cram | 742942590.0 | 5714943.0 | SC RUN 16164 8#7 | 0:55 1:75 | A:228799118;C:117009382;G:166056205;T:230565934;N:511951 | 55 | 75 | 228799118 | 117009382 | 166056205 | 230565934 | 511951 | ERX1065706 | ERS715215 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.19264 | 0.50767 | 0.1428 | 0.15173 | 0.9666 | 0.94606 | 0.57413 | 0.53902 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13317 | 13317 | ERR984484 | ERX1065705 | ERS715214 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367562 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:40:24Z|External Id:SAMEA3367562|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:40:24Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 6 sc 2286386|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo homozygous for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TGTGGTTG is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 6 sc 2286386|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#6 | 13741613 | Illumina sequencing of library 13741613 constructed from sample accession ERS715214 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TGTGGTTG. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#6.cram | cram | 908951420.0 | 6991934.0 | SC RUN 16164 8#6 | 0:55 1:75 | A:266807632;C:158160652;G:194742499;T:288619707;N:620930 | 55 | 75 | 266807632 | 158160652 | 194742499 | 288619707 | 620930 | ERX1065705 | ERS715214 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.20021 | 0.52069 | 0.13208 | 0.1197 | 0.95775 | 0.93324 | 0.52946 | 0.52456 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13318 | 13318 | ERR984483 | ERX1065704 | ERS715213 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367561 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:00:47Z|External Id:SAMEA3367561|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:00:47Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 5 sc 2286385|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo homozygous for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TCCTCAAT is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 5 sc 2286385|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#5 | 13741612 | Illumina sequencing of library 13741612 constructed from sample accession ERS715213 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TCCTCAAT. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#5.cram | cram | 771659330.0 | 5935841.0 | SC RUN 16164 8#5 | 0:55 1:75 | A:225161011;C:121434126;G:174639826;T:249876341;N:548026 | 55 | 75 | 225161011 | 121434126 | 174639826 | 249876341 | 548026 | ERX1065704 | ERS715213 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.21069 | 0.57513 | 0.14228 | 0.12501 | 0.95672 | 0.92488 | 0.54397 | 0.52111 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13319 | 13319 | ERR984482 | ERX1065703 | ERS715212 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367560 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:00:47Z|External Id:SAMEA3367560|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:00:47Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 4 sc 2286384|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo homozygous for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TACAGGAT is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 4 sc 2286384|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#4 | 13741611 | Illumina sequencing of library 13741611 constructed from sample accession ERS715212 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TACAGGAT. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#4.cram | cram | 784183790.0 | 6032183.0 | SC RUN 16164 8#4 | 0:55 1:75 | A:219327080;C:128313123;G:169475262;T:266538585;N:529740 | 55 | 75 | 219327080 | 128313123 | 169475262 | 266538585 | 529740 | ERX1065703 | ERS715212 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.20392 | 0.58702 | 0.12804 | 0.12156 | 0.96047 | 0.9133 | 0.61438 | 0.53735 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13320 | 13320 | ERR984481 | ERX1065702 | ERS715211 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367559 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:55Z|ENA LAST UPDATE:2018 03 09T00:40:24Z|External Id:SAMEA3367559|INSDC center name:SC|INSDC first public:2015 08 18T09:04:55Z|INSDC last update:2018 03 09T00:40:24Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 3 sc 2286383|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo homozygous for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TAGTGACT is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 3 sc 2286383|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#3 | 13741610 | Illumina sequencing of library 13741610 constructed from sample accession ERS715211 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TAGTGACT. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#3.cram | cram | 810265170.0 | 6232809.0 | SC RUN 16164 8#3 | 0:55 1:75 | A:237117705;C:130774361;G:170817877;T:270997878;N:557349 | 55 | 75 | 237117705 | 130774361 | 170817877 | 270997878 | 557349 | ERX1065702 | ERS715211 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.22414 | 0.5931 | 0.14561 | 0.13304 | 0.95651 | 0.91423 | 0.59465 | 0.54152 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13321 | 13321 | ERR984480 | ERX1065701 | ERS715210 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367558 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:55Z|ENA LAST UPDATE:2018 03 09T00:00:47Z|External Id:SAMEA3367558|INSDC center name:SC|INSDC first public:2015 08 18T09:04:55Z|INSDC last update:2018 03 09T00:00:47Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 2 sc 2286382|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo homozygous for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TTCCTGCT is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 2 sc 2286382|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#2 | 13741609 | Illumina sequencing of library 13741609 constructed from sample accession ERS715210 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TTCCTGCT. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#2.cram | cram | 698194770.0 | 5370729.0 | SC RUN 16164 8#2 | 0:55 1:75 | A:190784194;C:110138446;G:188418516;T:208362798;N:490816 | 55 | 75 | 190784194 | 110138446 | 188418516 | 208362798 | 490816 | ERX1065701 | ERS715210 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.17398 | 0.58306 | 0.10399 | 0.12476 | 0.96372 | 0.94468 | 0.64309 | 0.54721 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 13322 | 13322 | ERR984479 | ERX1065700 | ERS715209 | ERP006132 | PRJEB6584 | Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project | Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191 | Transcriptome Analysis | Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling. | SAMEA3367557 | SC | ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028 Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:00:47Z|External Id:SAMEA3367557|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:00:47Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 1 sc 2286381|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo homozygous for pcna allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TGCGATCT is bases 13 to 20 of read 1 followed by CG and 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/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 1 sc 2286381|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing | SC EXP 16164 8#1 | 13741608 | Illumina sequencing of library 13741608 constructed from sample accession ERS715209 for study accession ERP006132. This is part of an Illumina multiplexed sequencing run 16164 8. This submission includes reads tagged with the sequence TGCGATCT. | Transcriptome counting qPCR only | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | ERP006132 | Illumina HiSeq 2000 paired end sequencing | ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16 | 16164_8#1.cram | cram | 882032060.0 | 6784862.0 | SC RUN 16164 8#1 | 0:55 1:75 | A:258098215;C:144707482;G:194402683;T:284218124;N:605556 | 55 | 75 | 258098215 | 144707482 | 194402683 | 284218124 | 605556 | ERX1065700 | ERS715209 | ERA466416 | The Wellcome Trust Sanger Institute|European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.21585 | 0.55375 | 0.14409 | 0.13461 | 0.96015 | 0.9246 | 0.61791 | 0.5495 | 55 | 75 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2015-08-18 | Multi-stage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||
| 29053 | 29053 | SRR26990806 | SRX22683813 | SRS19677527 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | zebrafish itgavko tc 8d 3 | GSM7924146 | source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf|geo loc name:missing|collection date:missing | zebrafish itgavko tc 8d 3 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | whole fish with tailfin cut | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf | GSM7924146 | GSM7924146: zebrafish itgavko tc 8d 3; Danio rerio; RNA Seq | GSM7924146 r1 | GSM7924146 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 6_zebrafish_itgavko_tc_8d_3_S31_L001_R2_001.fastq.gz 6_zebrafish_itgavko_tc_8d_3_S31_L001_R1_001.fastq.gz | fastq fastq | 3875161320.0 | 12831660.0 | GSM7924146 r1 | 0:151 1:151 | A:1223303253;C:711567515;G:746979670;T:1193309732;N:1150 | 151 | 151 | 1223303253 | 711567515 | 746979670 | 1193309732 | 1150 | SRX22683813 | SRS19677527 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.84595 | 0.84551 | 0.30568 | 0.30506 | 0.77329 | 0.76948 | 0.63885 | 0.64046 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||
| 29054 | 29054 | SRR26990807 | SRX22683812 | SRS19677526 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | zebrafish itgavko tc 8d 2 | GSM7924145 | source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf|geo loc name:missing|collection date:missing | zebrafish itgavko tc 8d 2 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | whole fish with tailfin cut | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf | GSM7924145 | GSM7924145: zebrafish itgavko tc 8d 2; Danio rerio; RNA Seq | GSM7924145 r1 | GSM7924145 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 5_zebrafish_itgavko_tc_8d_2_S30_L001_R1_001.fastq.gz 5_zebrafish_itgavko_tc_8d_2_S30_L001_R2_001.fastq.gz | fastq fastq | 4365991652.0 | 14456926.0 | GSM7924145 r1 | 0:151 1:151 | A:1270600077;C:909032449;G:940039197;T:1246318704;N:1225 | 151 | 151 | 1270600077 | 909032449 | 940039197 | 1246318704 | 1225 | SRX22683812 | SRS19677526 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.91871 | 0.91856 | 0.21085 | 0.20755 | 0.71114 | 0.70873 | 0.45669 | 0.45984 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||
| 29055 | 29055 | SRR26990808 | SRX22683811 | SRS19677525 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | zebrafish itgavko tc 8d 1 | GSM7924144 | source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf|geo loc name:missing|collection date:missing | zebrafish itgavko tc 8d 1 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | whole fish with tailfin cut | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf | GSM7924144 | GSM7924144: zebrafish itgavko tc 8d 1; Danio rerio; RNA Seq | GSM7924144 r1 | GSM7924144 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 4_zebrafish_itgavko_tc_8d_1_S29_L001_R1_001.fastq.gz 4_zebrafish_itgavko_tc_8d_1_S29_L001_R2_001.fastq.gz | fastq fastq | 4802635634.0 | 15902767.0 | GSM7924144 r1 | 0:151 1:151 | A:1431003343;C:965403922;G:1003504713;T:1402722287;N:1369 | 151 | 151 | 1431003343 | 965403922 | 1003504713 | 1402722287 | 1369 | SRX22683811 | SRS19677525 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.90555 | 0.90464 | 0.24806 | 0.24593 | 0.72182 | 0.72007 | 0.46914 | 0.47508 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||
| 29056 | 29056 | SRR26990809 | SRX22683810 | SRS19677524 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | zebrafish wt tc 8d 3 | GSM7924143 | source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:wildtype|time:8dpf|geo loc name:missing|collection date:missing | zebrafish wt tc 8d 3 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | whole fish with tailfin cut | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:whole fish with tailfin cut|genotype:wildtype|time:8dpf | GSM7924143 | GSM7924143: zebrafish wt tc 8d 3; Danio rerio; RNA Seq | GSM7924143 r1 | GSM7924143 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 3_zebrafish_wt_tc_8d_3_S28_L001_R1_001.fastq.gz 3_zebrafish_wt_tc_8d_3_S28_L001_R2_001.fastq.gz | fastq fastq | 4510890648.0 | 14936724.0 | GSM7924143 r1 | 0:151 1:151 | A:1375725383;C:876879135;G:915216593;T:1343068155;N:1382 | 151 | 151 | 1375725383 | 876879135 | 915216593 | 1343068155 | 1382 | SRX22683810 | SRS19677524 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.87519 | 0.87203 | 0.27672 | 0.27432 | 0.74282 | 0.74054 | 0.54199 | 0.54873 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;