run_metadata
4,114 rows where devstage_curation = "Multi-stage"
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 | |||||||||||||||||||
| 9892 | 9892 | ERR4172795 | ERX4136409 | ERS4580819 | ERP121885 | PRJEB38455 | RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E-MTAB-9113 | Transcriptome Analysis | RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22 | Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion | sibling 3 | SAMEA6853229 | Centre for Developmental Neurobiology King's College London | ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853229|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sibling 3|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|sample name:E MTAB 9113:sibling 3|scientific name:Danio rerio | Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E MTAB 9113:sibling 3 p | sibling 3 p | RNA 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 constructed with ribodepletion | Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | ERP121885 | Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19 | UCLGNS1141-gfp-sibs-3_S6_R1.fastq.gz UCLGNS1141-gfp-sibs-3_S6_R2.fastq.gz | fastq fastq | E MTAB 9113:UCLGNS1141 gfp sibs 3 S6 R | 0:81 1:81 | A:1144578958;C:1113109875;G:1138809559;T:1117038434;N:213932 | 81 | 81 | 1144578958 | 1113109875 | 1138809559 | 1117038434 | 213932 | ERX4136409 | ERS4580819 | ERA2625401 | Centre for Developmental Neurobiology King | Centre for Developmental Neurobiology King | 2 | 0.96684 | 0.96492 | 0.03244 | 0.0317 | 0.71236 | 0.71514 | 0.45871 | 0.46189 | 81 | 81 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United Kingdom | 2020-05-22 | Multi-stage | Multi-stage | Embryo Imprecise | All anatomical structures | |||||||||||||||
| 9893 | 9893 | ERR4172794 | ERX4136408 | ERS4580818 | ERP121885 | PRJEB38455 | RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E-MTAB-9113 | Transcriptome Analysis | RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22 | Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion | sibling 2 | SAMEA6853228 | Centre for Developmental Neurobiology King's College London | ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853228|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sibling 2|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|sample name:E MTAB 9113:sibling 2|scientific name:Danio rerio | Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E MTAB 9113:sibling 2 p | sibling 2 p | RNA 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 constructed with ribodepletion | Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | ERP121885 | Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19 | UCLGNS1141-gfp-sibs-2_S4_R1.fastq.gz UCLGNS1141-gfp-sibs-2_S4_R2.fastq.gz | fastq fastq | E MTAB 9113:UCLGNS1141 gfp sibs 2 S4 R | 0:81 1:81 | A:1056280368;C:1036355469;G:1045429486;T:1035773622;N:189389 | 81 | 81 | 1056280368 | 1036355469 | 1045429486 | 1035773622 | 189389 | ERX4136408 | ERS4580818 | ERA2625401 | Centre for Developmental Neurobiology King | Centre for Developmental Neurobiology King | 2 | 0.95511 | 0.95696 | 0.02941 | 0.02903 | 0.71492 | 0.71628 | 0.45765 | 0.46537 | 81 | 81 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United Kingdom | 2020-05-22 | Multi-stage | Multi-stage | Embryo Imprecise | All anatomical structures | |||||||||||||||
| 9894 | 9894 | ERR4172793 | ERX4136407 | ERS4580817 | ERP121885 | PRJEB38455 | RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E-MTAB-9113 | Transcriptome Analysis | RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22 | Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion | sibling 1 | SAMEA6853227 | Centre for Developmental Neurobiology King's College London | ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853227|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sibling 1|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|sample name:E MTAB 9113:sibling 1|scientific name:Danio rerio | Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E MTAB 9113:sibling 1 p | sibling 1 p | RNA 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 constructed with ribodepletion | Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | ERP121885 | Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19 | UCLGNS1141-gfp-sibs-1_S2_R1.fastq.gz UCLGNS1141-gfp-sibs-1_S2_R2.fastq.gz | fastq fastq | E MTAB 9113:UCLGNS1141 gfp sibs 1 S2 R | 0:81 1:81 | A:1121176859;C:1093927654;G:1108608188;T:1101082277;N:209264 | 81 | 81 | 1121176859 | 1093927654 | 1108608188 | 1101082277 | 209264 | ERX4136407 | ERS4580817 | ERA2625401 | Centre for Developmental Neurobiology King | Centre for Developmental Neurobiology King | 2 | 0.95795 | 0.96004 | 0.02885 | 0.02854 | 0.71648 | 0.71756 | 0.44348 | 0.43956 | 81 | 81 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United Kingdom | 2020-05-22 | Multi-stage | Multi-stage | Embryo Imprecise | All anatomical structures | |||||||||||||||
| 9895 | 9895 | ERR4172792 | ERX4136406 | ERS4580816 | ERP121885 | PRJEB38455 | RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E-MTAB-9113 | Transcriptome Analysis | RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22 | Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion | sfpq 3 | SAMEA6853226 | Centre for Developmental Neurobiology King's College London | ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853226|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sfpq 3|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:sfpq / |sample name:E MTAB 9113:sfpq 3|scientific name:Danio rerio | Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E MTAB 9113:sfpq 3 p | sfpq 3 p | RNA 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 constructed with ribodepletion | Experimental Factor: genotype:sfpq / | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | ERP121885 | Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19 | UCLGNS1141-gfp-neg_3_S5_R1.fastq.gz UCLGNS1141-gfp-neg_3_S5_R2.fastq.gz | fastq fastq | E MTAB 9113:UCLGNS1141 gfp neg 3 S5 R | 0:81 1:81 | A:845849249;C:772302798;G:911660213;T:787409272;N:154042 | 81 | 81 | 845849249 | 772302798 | 911660213 | 787409272 | 154042 | ERX4136406 | ERS4580816 | ERA2625401 | Centre for Developmental Neurobiology King | Centre for Developmental Neurobiology King | 2 | 0.96298 | 0.95486 | 0.03415 | 0.03476 | 0.7167 | 0.73503 | 0.4665 | 0.45947 | 81 | 81 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United Kingdom | 2020-05-22 | Multi-stage | Multi-stage | Embryo Imprecise | All anatomical structures | |||||||||||||||
| 9896 | 9896 | ERR4172791 | ERX4136405 | ERS4580815 | ERP121885 | PRJEB38455 | RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E-MTAB-9113 | Transcriptome Analysis | RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22 | Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion | sfpq 2 | SAMEA6853225 | Centre for Developmental Neurobiology King's College London | ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853225|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sfpq 2|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:sfpq / |sample name:E MTAB 9113:sfpq 2|scientific name:Danio rerio | Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E MTAB 9113:sfpq 2 p | sfpq 2 p | RNA 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 constructed with ribodepletion | Experimental Factor: genotype:sfpq / | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | ERP121885 | Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19 | UCLGNS1141-gfp-neg-2_S3_R1.fastq.gz UCLGNS1141-gfp-neg-2_S3_R2.fastq.gz | fastq fastq | E MTAB 9113:UCLGNS1141 gfp neg 2 S3 R | 0:81 1:81 | A:961156886;C:917011292;G:942713581;T:936109877;N:157724 | 81 | 81 | 961156886 | 917011292 | 942713581 | 936109877 | 157724 | ERX4136405 | ERS4580815 | ERA2625401 | Centre for Developmental Neurobiology King | Centre for Developmental Neurobiology King | 2 | 0.96276 | 0.96147 | 0.03436 | 0.03382 | 0.71892 | 0.72021 | 0.4581 | 0.46402 | 81 | 81 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United Kingdom | 2020-05-22 | Multi-stage | Multi-stage | Embryo Imprecise | All anatomical structures | |||||||||||||||
| 9897 | 9897 | ERR4172790 | ERX4136404 | ERS4580814 | ERP121885 | PRJEB38455 | RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E-MTAB-9113 | Transcriptome Analysis | RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22 | Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion | sfpq 1 | SAMEA6853224 | Centre for Developmental Neurobiology King's College London | ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853224|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sfpq 1|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:sfpq / |sample name:E MTAB 9113:sfpq 1|scientific name:Danio rerio | Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | E MTAB 9113:sfpq 1 p | sfpq 1 p | RNA 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 constructed with ribodepletion | Experimental Factor: genotype:sfpq / | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | ERP121885 | Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf | ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19 | UCLGNS1141-gfp-neg-1_S1_R1.fastq.gz UCLGNS1141-gfp-neg-1_S1_R2.fastq.gz | fastq fastq | E MTAB 9113:UCLGNS1141 gfp neg 1 S1 R | 0:81 1:81 | A:1046317524;C:1014946275;G:1036910299;T:1023619857;N:185237 | 81 | 81 | 1046317524 | 1014946275 | 1036910299 | 1023619857 | 185237 | ERX4136404 | ERS4580814 | ERA2625401 | Centre for Developmental Neurobiology King | Centre for Developmental Neurobiology King | 2 | 0.96015 | 0.96173 | 0.03114 | 0.03098 | 0.7175 | 0.71865 | 0.46666 | 0.46399 | 81 | 81 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United Kingdom | 2020-05-22 | Multi-stage | Multi-stage | Embryo Imprecise | All anatomical structures | |||||||||||||||
| 9898 | 9898 | ERR4194114 | ERX4155254 | ERS4601292 | ERP122151 | PRJEB38705 | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E-MTAB-9193 | Transcriptome Analysis | TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately. | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Sample 2 | SAMEA6873729 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada | ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873729|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 2|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 2|scientific name:Danio rerio|sex:mixed | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E MTAB 9193:Sample 2 s | Sample 2 s | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Experimental Factor: age:8|Experimental Factor: RNA interference:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | ERP122151 | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | cDNA8h_1_S2_L001.bam | bam | 10087287534.0 | 99874134.0 | E MTAB 9193:cDNA8h 1 S2 L001 | 0:101 | A:2892833391;C:2022466595;G:2198646699;T:2962268446;N:11072403 | 101 | 2892833391 | 2022466595 | 2198646699 | 2962268446 | 11072403 | ERX4155254 | ERS4601292 | ERA2667966 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | 1 | 0.93609 | 0.12902 | 0.82158 | 0.5062 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Canada | 2020-06-04 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 9899 | 9899 | ERR4194115 | ERX4155254 | ERS4601292 | ERP122151 | PRJEB38705 | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E-MTAB-9193 | Transcriptome Analysis | TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately. | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Sample 2 | SAMEA6873729 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada | ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873729|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 2|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 2|scientific name:Danio rerio|sex:mixed | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E MTAB 9193:Sample 2 s | Sample 2 s | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Experimental Factor: age:8|Experimental Factor: RNA interference:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | ERP122151 | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | cDNA8h_1_S2_L002.bam | bam | 10191911414.0 | 100910014.0 | E MTAB 9193:cDNA8h 1 S2 L002 | 0:101 | A:2923216190;C:2043975715;G:2221734566;T:2992798366;N:10186577 | 101 | 2923216190 | 2043975715 | 2221734566 | 2992798366 | 10186577 | ERX4155254 | ERS4601292 | ERA2667966 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | 1 | 0.93445 | 0.13038 | 0.824 | 0.49774 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Canada | 2020-06-04 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 9900 | 9900 | ERR4194112 | ERX4155253 | ERS4601291 | ERP122151 | PRJEB38705 | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E-MTAB-9193 | Transcriptome Analysis | TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately. | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Sample 1 | SAMEA6873728 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada | ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873728|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 1|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 1|scientific name:Danio rerio|sex:mixed | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E MTAB 9193:Sample 1 s | Sample 1 s | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Experimental Factor: age:6|Experimental Factor: RNA interference:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | ERP122151 | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | cDNA6h_1_S1_L001.bam | bam | 7181772357.0 | 71106657.0 | E MTAB 9193:cDNA6h 1 S1 L001 | 0:101 | A:2074032710;C:1415439071;G:1544274166;T:2140112533;N:7913877 | 101 | 2074032710 | 1415439071 | 1544274166 | 2140112533 | 7913877 | ERX4155253 | ERS4601291 | ERA2667966 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | 1 | 0.9297 | 0.12156 | 0.8117 | 0.51457 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Canada | 2020-06-04 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 9901 | 9901 | ERR4194113 | ERX4155253 | ERS4601291 | ERP122151 | PRJEB38705 | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E-MTAB-9193 | Transcriptome Analysis | TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately. | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Sample 1 | SAMEA6873728 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada | ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873728|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 1|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 1|scientific name:Danio rerio|sex:mixed | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E MTAB 9193:Sample 1 s | Sample 1 s | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Experimental Factor: age:6|Experimental Factor: RNA interference:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | ERP122151 | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | cDNA6h_1_S1_L002.bam | bam | 7256542253.0 | 71846953.0 | E MTAB 9193:cDNA6h 1 S1 L002 | 0:101 | A:2096163385;C:1430325700;G:1560530043;T:2162265616;N:7257509 | 101 | 2096163385 | 1430325700 | 1560530043 | 2162265616 | 7257509 | ERX4155253 | ERS4601291 | ERA2667966 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | 1 | 0.92882 | 0.12127 | 0.81162 | 0.51457 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Canada | 2020-06-04 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 9902 | 9902 | ERR4194128 | ERX4155256 | ERS4601294 | ERP122151 | PRJEB38705 | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E-MTAB-9193 | Transcriptome Analysis | TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately. | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Sample 4 | SAMEA6873731 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada | ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873731|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 4|age:13|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 4|scientific name:Danio rerio|sex:mixed | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E MTAB 9193:Sample 4 s | Sample 4 s | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Experimental Factor: age:13|Experimental Factor: RNA interference:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | ERP122151 | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | cDNA13h_1_control_S1_L001.bam | bam | 10785974123.0 | 106791823.0 | E MTAB 9193:cDNA13h 1 control S1 L001 | 0:101 | A:3007305661;C:2241057062;G:2505494392;T:2986021199;N:46095809 | 101 | 3007305661 | 2241057062 | 2505494392 | 2986021199 | 46095809 | ERX4155256 | ERS4601294 | ERA2667966 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | 1 | 0.67094 | 0.07571 | 0.92951 | 0.5272 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Canada | 2020-06-04 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 9903 | 9903 | ERR4194129 | ERX4155256 | ERS4601294 | ERP122151 | PRJEB38705 | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E-MTAB-9193 | Transcriptome Analysis | TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately. | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Sample 4 | SAMEA6873731 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada | ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873731|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 4|age:13|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 4|scientific name:Danio rerio|sex:mixed | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E MTAB 9193:Sample 4 s | Sample 4 s | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Experimental Factor: age:13|Experimental Factor: RNA interference:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | ERP122151 | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | cDNA13h_1_control_S1_L002.bam | bam | 10595192294.0 | 104902894.0 | E MTAB 9193:cDNA13h 1 control S1 L002 | 0:101 | A:2971916419;C:2204229263;G:2390854035;T:2949877754;N:78314823 | 101 | 2971916419 | 2204229263 | 2390854035 | 2949877754 | 78314823 | ERX4155256 | ERS4601294 | ERA2667966 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | 1 | 0.67255 | 0.08054 | 0.91583 | 0.52661 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Canada | 2020-06-04 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 9904 | 9904 | ERR4194116 | ERX4155255 | ERS4601293 | ERP122151 | PRJEB38705 | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E-MTAB-9193 | Transcriptome Analysis | TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately. | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Sample 3 | SAMEA6873730 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada | ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E MTAB 9193:Sample 3 s | Sample 3 s | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Experimental Factor: age:10|Experimental Factor: RNA interference:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | ERP122151 | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | cDNA10h_1_S3_L001.bam | bam | 1622536412.0 | 16556494.0 | E MTAB 9193:cDNA10h 1 S3 L001 | 0:98 | A:491141175;C:317161060;G:354179755;T:459976409;N:78013 | 98 | 491141175 | 317161060 | 354179755 | 459976409 | 78013 | ERX4155255 | ERS4601293 | ERA2667966 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | 1 | 0.93238 | 0.13033 | 0.89132 | 0.47076 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Canada | 2020-06-04 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 9905 | 9905 | ERR4194117 | ERX4155255 | ERS4601293 | ERP122151 | PRJEB38705 | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E-MTAB-9193 | Transcriptome Analysis | TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately. | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Sample 3 | SAMEA6873730 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada | ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E MTAB 9193:Sample 3 s | Sample 3 s | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Experimental Factor: age:10|Experimental Factor: RNA interference:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | ERP122151 | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | cDNA10h_1_S3_L002.bam | bam | 1484328776.0 | 15146212.0 | E MTAB 9193:cDNA10h 1 S3 L002 | 0:98 | A:450782055;C:290088574;G:322801188;T:420570801;N:86158 | 98 | 450782055 | 290088574 | 322801188 | 420570801 | 86158 | ERX4155255 | ERS4601293 | ERA2667966 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | 1 | 0.92846 | 0.13128 | 0.89923 | 0.46879 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Canada | 2020-06-04 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 9906 | 9906 | ERR4194118 | ERX4155255 | ERS4601293 | ERP122151 | PRJEB38705 | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E-MTAB-9193 | Transcriptome Analysis | TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately. | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Sample 3 | SAMEA6873730 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada | ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E MTAB 9193:Sample 3 s | Sample 3 s | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Experimental Factor: age:10|Experimental Factor: RNA interference:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | ERP122151 | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | cDNA10h_1_S3_L003.bam | bam | 1578833116.0 | 16110542.0 | E MTAB 9193:cDNA10h 1 S3 L003 | 0:98 | A:477600666;C:308260969;G:347303289;T:445467384;N:200808 | 98 | 477600666 | 308260969 | 347303289 | 445467384 | 200808 | ERX4155255 | ERS4601293 | ERA2667966 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | 1 | 0.93107 | 0.12965 | 0.91265 | 0.47375 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Canada | 2020-06-04 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 9907 | 9907 | ERR4194119 | ERX4155255 | ERS4601293 | ERP122151 | PRJEB38705 | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E-MTAB-9193 | Transcriptome Analysis | TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately. | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Sample 3 | SAMEA6873730 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada | ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E MTAB 9193:Sample 3 s | Sample 3 s | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Experimental Factor: age:10|Experimental Factor: RNA interference:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | ERP122151 | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | cDNA10h_1_S3_L004.bam | bam | 1859564994.0 | 18975153.0 | E MTAB 9193:cDNA10h 1 S3 L004 | 0:98 | A:562936790;C:364057256;G:406607636;T:525811595;N:151717 | 98 | 562936790 | 364057256 | 406607636 | 525811595 | 151717 | ERX4155255 | ERS4601293 | ERA2667966 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | 1 | 0.93453 | 0.1266 | 0.87714 | 0.46957 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Canada | 2020-06-04 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 9908 | 9908 | ERR4194120 | ERX4155255 | ERS4601293 | ERP122151 | PRJEB38705 | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E-MTAB-9193 | Transcriptome Analysis | TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately. | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Sample 3 | SAMEA6873730 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada | ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E MTAB 9193:Sample 3 s | Sample 3 s | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Experimental Factor: age:10|Experimental Factor: RNA interference:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | ERP122151 | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | cDNA10h_2_S3_L001.bam | bam | 1156341102.0 | 11799399.0 | E MTAB 9193:cDNA10h 2 S3 L001 | 0:98 | A:345857612;C:224453195;G:257551986;T:327969064;N:509245 | 98 | 345857612 | 224453195 | 257551986 | 327969064 | 509245 | ERX4155255 | ERS4601293 | ERA2667966 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | 1 | 0.93863 | 0.10744 | 0.81984 | 0.501 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Canada | 2020-06-04 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 9909 | 9909 | ERR4194121 | ERX4155255 | ERS4601293 | ERP122151 | PRJEB38705 | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E-MTAB-9193 | Transcriptome Analysis | TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately. | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Sample 3 | SAMEA6873730 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada | ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E MTAB 9193:Sample 3 s | Sample 3 s | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Experimental Factor: age:10|Experimental Factor: RNA interference:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | ERP122151 | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | cDNA10h_2_S3_L002.bam | bam | 1105219696.0 | 11277752.0 | E MTAB 9193:cDNA10h 2 S3 L002 | 0:98 | A:331051973;C:214369903;G:246546338;T:312897773;N:353709 | 98 | 331051973 | 214369903 | 246546338 | 312897773 | 353709 | ERX4155255 | ERS4601293 | ERA2667966 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | 1 | 0.93941 | 0.10818 | 0.82211 | 0.50079 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Canada | 2020-06-04 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 9910 | 9910 | ERR4194122 | ERX4155255 | ERS4601293 | ERP122151 | PRJEB38705 | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E-MTAB-9193 | Transcriptome Analysis | TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately. | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Sample 3 | SAMEA6873730 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada | ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E MTAB 9193:Sample 3 s | Sample 3 s | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Experimental Factor: age:10|Experimental Factor: RNA interference:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | ERP122151 | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | cDNA10h_2_S3_L003.bam | bam | 1105199606.0 | 11277547.0 | E MTAB 9193:cDNA10h 2 S3 L003 | 0:98 | A:331158619;C:214305131;G:246465559;T:312930408;N:339889 | 98 | 331158619 | 214305131 | 246465559 | 312930408 | 339889 | ERX4155255 | ERS4601293 | ERA2667966 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | 1 | 0.93767 | 0.10645 | 0.82329 | 0.50057 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Canada | 2020-06-04 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 9911 | 9911 | ERR4194123 | ERX4155255 | ERS4601293 | ERP122151 | PRJEB38705 | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E-MTAB-9193 | Transcriptome Analysis | TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately. | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Sample 3 | SAMEA6873730 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada | ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E MTAB 9193:Sample 3 s | Sample 3 s | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Experimental Factor: age:10|Experimental Factor: RNA interference:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | ERP122151 | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | cDNA10h_2_S3_L004.bam | bam | 1108707712.0 | 11313344.0 | E MTAB 9193:cDNA10h 2 S3 L004 | 0:98 | A:331374433;C:215925150;G:247131942;T:313865174;N:411013 | 98 | 331374433 | 215925150 | 247131942 | 313865174 | 411013 | ERX4155255 | ERS4601293 | ERA2667966 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | 1 | 0.93827 | 0.10842 | 0.82031 | 0.49241 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Canada | 2020-06-04 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 9912 | 9912 | ERR4194124 | ERX4155255 | ERS4601293 | ERP122151 | PRJEB38705 | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E-MTAB-9193 | Transcriptome Analysis | TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately. | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Sample 3 | SAMEA6873730 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada | ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E MTAB 9193:Sample 3 s | Sample 3 s | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Experimental Factor: age:10|Experimental Factor: RNA interference:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | ERP122151 | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | cDNA10h_2_S3_L005.bam | bam | 1110084612.0 | 11327394.0 | E MTAB 9193:cDNA10h 2 S3 L005 | 0:98 | A:332881960;C:215360330;G:247563319;T:313842331;N:436672 | 98 | 332881960 | 215360330 | 247563319 | 313842331 | 436672 | ERX4155255 | ERS4601293 | ERA2667966 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | 1 | 0.93827 | 0.10719 | 0.8238 | 0.50406 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Canada | 2020-06-04 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 9913 | 9913 | ERR4194125 | ERX4155255 | ERS4601293 | ERP122151 | PRJEB38705 | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E-MTAB-9193 | Transcriptome Analysis | TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately. | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Sample 3 | SAMEA6873730 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada | ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E MTAB 9193:Sample 3 s | Sample 3 s | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Experimental Factor: age:10|Experimental Factor: RNA interference:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | ERP122151 | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | cDNA10h_2_S3_L006.bam | bam | 1113812728.0 | 11365436.0 | E MTAB 9193:cDNA10h 2 S3 L006 | 0:98 | A:333112288;C:216649152;G:248341020;T:315338848;N:371420 | 98 | 333112288 | 216649152 | 248341020 | 315338848 | 371420 | ERX4155255 | ERS4601293 | ERA2667966 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | 1 | 0.93843 | 0.10675 | 0.82079 | 0.49284 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Canada | 2020-06-04 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 9914 | 9914 | ERR4194126 | ERX4155255 | ERS4601293 | ERP122151 | PRJEB38705 | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E-MTAB-9193 | Transcriptome Analysis | TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately. | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Sample 3 | SAMEA6873730 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada | ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E MTAB 9193:Sample 3 s | Sample 3 s | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Experimental Factor: age:10|Experimental Factor: RNA interference:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | ERP122151 | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | cDNA10h_2_S3_L007.bam | bam | 1119495748.0 | 11423426.0 | E MTAB 9193:cDNA10h 2 S3 L007 | 0:98 | A:335288339;C:217283719;G:249624836;T:316900388;N:398466 | 98 | 335288339 | 217283719 | 249624836 | 316900388 | 398466 | ERX4155255 | ERS4601293 | ERA2667966 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | 1 | 0.93711 | 0.10749 | 0.82266 | 0.49382 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Canada | 2020-06-04 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 9915 | 9915 | ERR4194127 | ERX4155255 | ERS4601293 | ERP122151 | PRJEB38705 | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E-MTAB-9193 | Transcriptome Analysis | TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately. | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Sample 3 | SAMEA6873730 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada | ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E MTAB 9193:Sample 3 s | Sample 3 s | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Experimental Factor: age:10|Experimental Factor: RNA interference:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | ERP122151 | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | cDNA10h_2_S3_L008.bam | bam | 1175946688.0 | 11999456.0 | E MTAB 9193:cDNA10h 2 S3 L008 | 0:98 | A:351364169;C:228318193;G:261971072;T:333863943;N:429311 | 98 | 351364169 | 228318193 | 261971072 | 333863943 | 429311 | ERX4155255 | ERS4601293 | ERA2667966 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | 1 | 0.93851 | 0.10755 | 0.82158 | 0.49895 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Canada | 2020-06-04 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 9916 | 9916 | ERR4194130 | ERX4155257 | ERS4601295 | ERP122151 | PRJEB38705 | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E-MTAB-9193 | Transcriptome Analysis | TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately. | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Sample 5 | SAMEA6873732 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada | ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873732|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 5|age:13|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 5|scientific name:Danio rerio|sex:mixed | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E MTAB 9193:Sample 5 s | Sample 5 s | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Experimental Factor: age:13|Experimental Factor: RNA interference:morpholino mediated Gata5/6 knockdown | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | ERP122151 | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | cDNA13h_2_gata56KD_S2_L001.bam | bam | 7791309377.0 | 77141677.0 | E MTAB 9193:cDNA13h 2 gata56KD S2 L001 | 0:101 | A:2198242220;C:1593746618;G:1784167452;T:2181979820;N:33173267 | 101 | 2198242220 | 1593746618 | 1784167452 | 2181979820 | 33173267 | ERX4155257 | ERS4601295 | ERA2667966 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | 1 | 0.66736 | 0.08039 | 0.93026 | 0.50796 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Canada | 2020-06-04 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 9917 | 9917 | ERR4194131 | ERX4155257 | ERS4601295 | ERP122151 | PRJEB38705 | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E-MTAB-9193 | Transcriptome Analysis | TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately. | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Sample 5 | SAMEA6873732 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada | ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873732|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 5|age:13|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 5|scientific name:Danio rerio|sex:mixed | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | E MTAB 9193:Sample 5 s | Sample 5 s | Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry. | Experimental Factor: age:13|Experimental Factor: RNA interference:morpholino mediated Gata5/6 knockdown | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | ERP122151 | Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish | ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01 | cDNA13h_2_gata56KD_S2_L002.bam | bam | 7658149967.0 | 75823267.0 | E MTAB 9193:cDNA13h 2 gata56KD S2 L002 | 0:101 | A:2172230233;C:1568805100;G:1703587704;T:2157181071;N:56345859 | 101 | 2172230233 | 1568805100 | 1703587704 | 2157181071 | 56345859 | ERX4155257 | ERS4601295 | ERA2667966 | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive | 1 | 0.66565 | 0.08597 | 0.91804 | 0.51772 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Canada | 2020-06-04 | Multi-stage | Embryo | Embryo Imprecise | 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 | |||||||||||||||||||||
| 10213 | 10213 | ERR6511329 | ERX6138165 | ERS7264188 | ERP131213 | PRJEB46978 | Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing | ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159 | Other | Nano3P seq is a simple and robust method to accurately estimate transcript levels tail lengths and tail nucleotide composition information in full length individual reads with minimal library preparation biases both in the coding and non coding transcriptome. | ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28 | Zebrafish Nano3P seq of Ribodepleted sample biological replicate 1 including 2 hpf 4 hpf 6 hpf RNAs | Zebrafish Ribodep Rep1 | SAMEA9541418 | CENTER FOR GENOMIC REGULATION (CRG) | ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541418|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish Ribodep Rep1|common name:zebrafish|sample name:Zebrafish Ribodep Rep1|scientific name:Danio rerio | MinION sequencing | ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 3 | cDNA786327 | Nano3P seq | Nano3P seq | OTHER | TRANSCRIPTOMIC | unspecified | SINGLE | OXFORD_NANOPORE | MinION | ERP131213 | MinION sequencing | ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28 | zebrafish_ribodep_rep1.tar.gz | nanopore | 1745399583.0 | 1644167.0 | ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 3 | 0:1061.57 | A:449704009;C:421915878;G:378879857;T:494899839;N:0 | 1061 | 449704009 | 421915878 | 378879857 | 494899839 | 0 | ERX6138165 | ERS7264188 | ERA5757997 | CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive | CENTER FOR GENOMIC REGULATION (CRG) | 1 | 0.01112 | 0.0 | 0.99997 | 1.0 | 546 | T | long read | ont | ont | full_length | rrna_depletion | unknown | bulk | unknown | unknown | Spain | 2023-12-28 | Multi-stage | Embryo | Undetermined | Embryo Imprecise | |||||||||||||||||||||
| 10215 | 10215 | ERR6511330 | ERX6138166 | ERS7264189 | ERP131213 | PRJEB46978 | Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing | ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159 | Other | Nano3P seq is a simple and robust method to accurately estimate transcript levels tail lengths and tail nucleotide composition information in full length individual reads with minimal library preparation biases both in the coding and non coding transcriptome. | ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28 | Zebrafish Nano3P seq of Ribodepleted sample biological replicate 1 including 2 hpf 4 hpf 6 hpf RNAs | Zebrafish Ribodep Rep2 | SAMEA9541419 | CENTER FOR GENOMIC REGULATION (CRG) | ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541419|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish Ribodep Rep2|common name:zebrafish|sample name:Zebrafish Ribodep Rep2|scientific name:Danio rerio | MinION sequencing | ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 4 | cDNA123791 | Nano3P seq | Nano3P seq | OTHER | TRANSCRIPTOMIC | unspecified | SINGLE | OXFORD_NANOPORE | MinION | ERP131213 | MinION sequencing | ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28 | zebrafish_ribodep_rep2.tar.gz | nanopore | 2038398139.0 | 1955617.0 | ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 4 | 0:1042.33 | A:518369802;C:477535545;G:441294056;T:601198736;N:0 | 1042 | 518369802 | 477535545 | 441294056 | 601198736 | 0 | ERX6138166 | ERS7264189 | ERA5757997 | CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive | CENTER FOR GENOMIC REGULATION (CRG) | ont | ont | full_length | rrna_depletion | unknown | bulk | unknown | unknown | Spain | 2023-12-28 | Multi-stage | Embryo | Undetermined | Embryo Imprecise | |||||||||||||||||||||||||||||
| 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 | ||||||||||||||||||||
| 11042 | 11042 | ERR9839781 | ERX9385638 | ERS12199238 | ERP138294 | PRJEB53494 | Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing | 94bf5509-4622-4d5f-b7c5-6a14bdfac340 | Other | RNA polyadenylation plays a central role in RNA maturation fate and stability. In response to developmental cues polyA tail lengths can vary affecting the translation efficiency and stability of mRNAs. Here we develop Nanopore three prime end capture sequencing Nano3P seq a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol Nano3P seq can sequence any given RNA molecule from its three prime end regardless of its polyadenylation status without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes providing quantitative estimates of RNA abundance and tail lengths in mRNA lncRNA sn/snoRNA scaRNA and rRNA molecules. We find that in addition to mRNA and lncRNA polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level correlating with mRNA decay. Finally we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis. Overall Nano3P seq is a simple and robust method for accurately estimating transcript levels tail lengths and tail composition heterogeneity in individual reads with minimal library preparation biases both in the coding and non coding transcriptome. | ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 | Zebrafish Ribodepleted RNA 2hpf 4hpf 6hpf | Zebrafish Ribodepleted Rep3 | SAMEA110100413 | CENTER FOR GENOMIC REGULATION (CRG) | ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100413|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish Ribodepleted Rep3|common name:zebrafish|sample name:Zebrafish Ribodepleted Rep3 | MinION sequencing | ena EXPERIMENT TAB 13 06 2022 16:07:52:807 817 | cDNA897892 ZFRDR3 | 1 | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | OXFORD_NANOPORE | MinION | ERP138294 | MinION sequencing | ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 | cDNA897892_ZFRDR3.tar.gz | nanopore | 848659575.0 | 587586.0 | ena RUN TAB 13 06 2022 16:07:52:808 818 | 0:1444.32 | A:210205014;C:186527780;G:188214279;T:263712502;N:0 | 1444 | 210205014 | 186527780 | 188214279 | 263712502 | 0 | ERX9385638 | ERS12199238 | ERA15547404 | CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive | CENTER FOR GENOMIC REGULATION (CRG) | ont | ont | 3prime | poly_a | unknown | bulk | unknown | unknown | Spain | 2022-10-10 | Multi-stage | Embryo | Undetermined | Embryo Imprecise | ||||||||||||||||||||||||||||||
| 11043 | 11043 | ERR9839780 | ERX9385637 | ERS12199237 | ERP138294 | PRJEB53494 | Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing | 94bf5509-4622-4d5f-b7c5-6a14bdfac340 | Other | RNA polyadenylation plays a central role in RNA maturation fate and stability. In response to developmental cues polyA tail lengths can vary affecting the translation efficiency and stability of mRNAs. Here we develop Nanopore three prime end capture sequencing Nano3P seq a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol Nano3P seq can sequence any given RNA molecule from its three prime end regardless of its polyadenylation status without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes providing quantitative estimates of RNA abundance and tail lengths in mRNA lncRNA sn/snoRNA scaRNA and rRNA molecules. We find that in addition to mRNA and lncRNA polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level correlating with mRNA decay. Finally we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis. Overall Nano3P seq is a simple and robust method for accurately estimating transcript levels tail lengths and tail composition heterogeneity in individual reads with minimal library preparation biases both in the coding and non coding transcriptome. | ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 | Zebrafish Ribodepleted RNA 2hpf 4hpf 6hpf | Zebrafish Ribodepleted Rep2 | SAMEA110100412 | CENTER FOR GENOMIC REGULATION (CRG) | ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100412|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish Ribodepleted Rep2|common name:zebrafish|sample name:Zebrafish Ribodepleted Rep2 | MinION sequencing | ena EXPERIMENT TAB 13 06 2022 16:07:52:807 815 | cDNA123791 ZFRDR2 | 1 | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | OXFORD_NANOPORE | MinION | ERP138294 | MinION sequencing | ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 | cDNA123791_ZFRDR2.tar.gz | nanopore | 2229275175.0 | 1955617.0 | ena RUN TAB 13 06 2022 16:07:52:807 816 | 0:1139.93 | A:533543922;C:498938137;G:515833119;T:680959997;N:0 | 1139 | 533543922 | 498938137 | 515833119 | 680959997 | 0 | ERX9385637 | ERS12199237 | ERA15547404 | CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive | CENTER FOR GENOMIC REGULATION (CRG) | ont | ont | 3prime | poly_a | unknown | bulk | unknown | unknown | Spain | 2022-10-10 | Multi-stage | Embryo | Undetermined | Embryo Imprecise | ||||||||||||||||||||||||||||||
| 11044 | 11044 | ERR9839779 | ERX9385636 | ERS12199236 | ERP138294 | PRJEB53494 | Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing | 94bf5509-4622-4d5f-b7c5-6a14bdfac340 | Other | RNA polyadenylation plays a central role in RNA maturation fate and stability. In response to developmental cues polyA tail lengths can vary affecting the translation efficiency and stability of mRNAs. Here we develop Nanopore three prime end capture sequencing Nano3P seq a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol Nano3P seq can sequence any given RNA molecule from its three prime end regardless of its polyadenylation status without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes providing quantitative estimates of RNA abundance and tail lengths in mRNA lncRNA sn/snoRNA scaRNA and rRNA molecules. We find that in addition to mRNA and lncRNA polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level correlating with mRNA decay. Finally we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis. Overall Nano3P seq is a simple and robust method for accurately estimating transcript levels tail lengths and tail composition heterogeneity in individual reads with minimal library preparation biases both in the coding and non coding transcriptome. | ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 | Zebrafish Ribodepleted RNA 2hpf 4hpf 6hpf | Zebrafish Ribodepleted Rep1 | SAMEA110100411 | CENTER FOR GENOMIC REGULATION (CRG) | ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100411|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish Ribodepleted Rep1|common name:zebrafish|sample name:Zebrafish Ribodepleted Rep1 | MinION sequencing | ena EXPERIMENT TAB 13 06 2022 16:07:52:807 813 | cDNA786327 ZFRDR1 | 1 | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | OXFORD_NANOPORE | MinION | ERP138294 | MinION sequencing | ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 | cDNA786327_ZFRDR1.tar.gz | nanopore | 1900613556.0 | 1660167.0 | ena RUN TAB 13 06 2022 16:07:52:807 814 | 0:1144.83 | A:473050820;C:438054520;G:425169743;T:564338473;N:0 | 1144 | 473050820 | 438054520 | 425169743 | 564338473 | 0 | ERX9385636 | ERS12199236 | ERA15547404 | CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive | CENTER FOR GENOMIC REGULATION (CRG) | ont | ont | 3prime | poly_a | unknown | bulk | unknown | unknown | Spain | 2022-10-10 | Multi-stage | Embryo | Undetermined | Embryo Imprecise | ||||||||||||||||||||||||||||||
| 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 |
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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");;