run_metadata
1,700 rows where devstage_curation_coarse = "Multi-stage" and experiment.library_layout = "PAIRED"
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 | |||||||||||||||
| 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 | |||||||||||||||
| 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 | |||||||||||||||
| 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 | |||||||||||||||
| 11821 | 11821 | ERR11834690 | ERX11232843 | ERS16254762 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 4 | SAMEA114265804 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265804|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 4|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250|organism part:whole organism|rin:9.6|sample name:E MTAB 13263:Sample 4|scientific name:Danio rerio|sex:na|stimulus:immunosuppression|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 4 p | Sample 4 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2113_dre_C1_clobetasolpropionate_lib667285_10169_3_2.fastq.gz NG-32417_R2113_dre_C1_clobetasolpropionate_lib667285_10169_3_1.fastq.gz | fastq fastq | 9764006696.0 | 32331148.0 | E MTAB 13263:NG 32417 R2113 dre C1 clobetasolpropionate lib667285 10169 3 | 0:151 1:151 | A:2627275848;C:2223323771;G:2323190525;T:2590103027;N:113525 | 151 | 151 | 2627275848 | 2223323771 | 2323190525 | 2590103027 | 113525 | ERX11232843 | ERS16254762 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.95424 | 0.95502 | 0.12596 | 0.12401 | 0.65884 | 0.65825 | 0.48134 | 0.48327 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11822 | 11822 | ERR11834689 | ERX11232842 | ERS16254761 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 3 | SAMEA114265803 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265803|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 3|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:0|organism part:whole organism|rin:9.4|sample name:E MTAB 13263:Sample 3|scientific name:Danio rerio|sex:na|stimulus:n1|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 3 p | Sample 3 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2112_dre_nc_clobetasolpropionate_lib673071_10180_1_2.fastq.gz NG-32417_R2112_dre_nc_clobetasolpropionate_lib673071_10180_1_1.fastq.gz | fastq fastq | 13326663550.0 | 44128025.0 | E MTAB 13263:NG 32417 R2112 dre nc clobetasolpropionate lib673071 10180 1 | 0:151 1:151 | A:3641640344;C:3020489123;G:3072643196;T:3591659412;N:231475 | 151 | 151 | 3641640344 | 3020489123 | 3072643196 | 3591659412 | 231475 | ERX11232842 | ERS16254761 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.95271 | 0.95293 | 0.11945 | 0.1151 | 0.65819 | 0.6579 | 0.47257 | 0.47803 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11823 | 11823 | ERR11834684 | ERX11232837 | ERS16254756 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 1 | SAMEA114265798 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265798|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 1|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:0|organism part:whole organism|rin:9.3|sample name:E MTAB 13263:Sample 1|scientific name:Danio rerio|sex:na|stimulus:n1|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 1 p | Sample 1 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2110_dre_nc_clobetasolpropionate_lib667282_10169_3_1.fastq.gz NG-32417_R2110_dre_nc_clobetasolpropionate_lib667282_10169_3_2.fastq.gz | fastq fastq | 10152616370.0 | 33617935.0 | E MTAB 13263:NG 32417 R2110 dre nc clobetasolpropionate lib667282 10169 3 | 0:151 1:151 | A:2743478864;C:2319134955;G:2378048842;T:2711839167;N:114542 | 151 | 151 | 2743478864 | 2319134955 | 2378048842 | 2711839167 | 114542 | ERX11232837 | ERS16254756 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.95273 | 0.95457 | 0.13567 | 0.13174 | 0.65896 | 0.65841 | 0.47947 | 0.47815 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11824 | 11824 | ERR11834691 | ERX11232844 | ERS16254763 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 5 | SAMEA114265805 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265805|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 5|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250|organism part:whole organism|rin:9.2|sample name:E MTAB 13263:Sample 5|scientific name:Danio rerio|sex:na|stimulus:immunosuppression|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 5 p | Sample 5 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2114_dre_C1_clobetasolpropionate_lib667286_10169_3_1.fastq.gz NG-32417_R2114_dre_C1_clobetasolpropionate_lib667286_10169_3_2.fastq.gz | fastq fastq | 11690304334.0 | 38709617.0 | E MTAB 13263:NG 32417 R2114 dre C1 clobetasolpropionate lib667286 10169 3 | 0:151 1:151 | A:3142106866;C:2677986743;G:2767050957;T:3103028799;N:130969 | 151 | 151 | 3142106866 | 2677986743 | 2767050957 | 3103028799 | 130969 | ERX11232844 | ERS16254763 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.95418 | 0.95523 | 0.12548 | 0.12397 | 0.66026 | 0.66016 | 0.46767 | 0.47253 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11825 | 11825 | ERR11834688 | ERX11232841 | ERS16254760 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 2 | SAMEA114265802 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265802|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 2|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:0|organism part:whole organism|rin:9.6|sample name:E MTAB 13263:Sample 2|scientific name:Danio rerio|sex:na|stimulus:n1|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 2 p | Sample 2 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2111_dre_nc_clobetasolpropionate_lib673070_10180_1_1.fastq.gz NG-32417_R2111_dre_nc_clobetasolpropionate_lib673070_10180_1_2.fastq.gz | fastq fastq | 11827163184.0 | 39162792.0 | E MTAB 13263:NG 32417 R2111 dre nc clobetasolpropionate lib673070 10180 1 | 0:151 1:151 | A:3256286612;C:2657918302;G:2701905502;T:3210846546;N:206222 | 151 | 151 | 3256286612 | 2657918302 | 2701905502 | 3210846546 | 206222 | ERX11232841 | ERS16254760 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.95203 | 0.95292 | 0.12277 | 0.11772 | 0.66048 | 0.65837 | 0.47243 | 0.4729 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11826 | 11826 | ERR11834693 | ERX11232846 | ERS16254765 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 7 | SAMEA114265807 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265807|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 7|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:4000|organism part:whole organism|rin:9.7|sample name:E MTAB 13263:Sample 7|scientific name:Danio rerio|sex:na|stimulus:immunostimulation|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 7 p | Sample 7 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2116_dre_nc_imq_clobetasolpropionate_lib667288_10169_3_1.fastq.gz NG-32417_R2116_dre_nc_imq_clobetasolpropionate_lib667288_10169_3_2.fastq.gz | fastq fastq | 11114382784.0 | 36802592.0 | E MTAB 13263:NG 32417 R2116 dre nc imq clobetasolpropionate lib667288 10169 3 | 0:151 1:151 | A:2997376944;C:2547742011;G:2613273908;T:2955864850;N:125071 | 151 | 151 | 2997376944 | 2547742011 | 2613273908 | 2955864850 | 125071 | ERX11232846 | ERS16254765 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.95392 | 0.9539 | 0.12951 | 0.12707 | 0.65628 | 0.65731 | 0.48132 | 0.48179 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11827 | 11827 | ERR11834695 | ERX11232848 | ERS16254767 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 9 | SAMEA114265809 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265809|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 9|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:4000|organism part:whole organism|rin:9.9|sample name:E MTAB 13263:Sample 9|scientific name:Danio rerio|sex:na|stimulus:immunostimulation|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 9 p | Sample 9 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2118_dre_nc_imq_clobetasolpropionate_lib667290_10169_3_1.fastq.gz NG-32417_R2118_dre_nc_imq_clobetasolpropionate_lib667290_10169_3_2.fastq.gz | fastq fastq | 9422294300.0 | 31199650.0 | E MTAB 13263:NG 32417 R2118 dre nc imq clobetasolpropionate lib667290 10169 3 | 0:151 1:151 | A:2541445212;C:2157798531;G:2214381344;T:2508560588;N:108625 | 151 | 151 | 2541445212 | 2157798531 | 2214381344 | 2508560588 | 108625 | ERX11232848 | ERS16254767 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.95337 | 0.95433 | 0.13046 | 0.12718 | 0.65845 | 0.65815 | 0.48198 | 0.48414 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11828 | 11828 | ERR11834687 | ERX11232840 | ERS16254759 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 12 | SAMEA114265801 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265801|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 12|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250 CP + 4000 IMQ|organism part:whole organism|rin:9.7|sample name:E MTAB 13263:Sample 12|scientific name:Danio rerio|sex:na|stimulus:immunosuppression and immunostimulation|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 12 p | Sample 12 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2121_dre_C1_imq_clobetasolpropionate_lib667293_10169_3_2.fastq.gz NG-32417_R2121_dre_C1_imq_clobetasolpropionate_lib667293_10169_3_1.fastq.gz | fastq fastq | 9285032280.0 | 30745140.0 | E MTAB 13263:NG 32417 R2121 dre C1 imq clobetasolpropionate lib667293 10169 3 | 0:151 1:151 | A:2504765552;C:2110325477;G:2196928032;T:2472905759;N:107460 | 151 | 151 | 2504765552 | 2110325477 | 2196928032 | 2472905759 | 107460 | ERX11232840 | ERS16254759 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.95411 | 0.95451 | 0.12502 | 0.12228 | 0.65829 | 0.65774 | 0.48259 | 0.47946 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11829 | 11829 | ERR11834694 | ERX11232847 | ERS16254766 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 8 | SAMEA114265808 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265808|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 8|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:4000|organism part:whole organism|rin:9.5|sample name:E MTAB 13263:Sample 8|scientific name:Danio rerio|sex:na|stimulus:immunostimulation|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 8 p | Sample 8 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2117_dre_nc_imq_clobetasolpropionate_lib667289_10169_3_1.fastq.gz NG-32417_R2117_dre_nc_imq_clobetasolpropionate_lib667289_10169_3_2.fastq.gz | fastq fastq | 10247527118.0 | 33932209.0 | E MTAB 13263:NG 32417 R2117 dre nc imq clobetasolpropionate lib667289 10169 3 | 0:151 1:151 | A:2766675319;C:2342307825;G:2405294253;T:2733131648;N:118073 | 151 | 151 | 2766675319 | 2342307825 | 2405294253 | 2733131648 | 118073 | ERX11232847 | ERS16254766 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.9541 | 0.95434 | 0.13364 | 0.13098 | 0.6576 | 0.6565 | 0.48068 | 0.48029 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11830 | 11830 | ERR11834692 | ERX11232845 | ERS16254764 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 6 | SAMEA114265806 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265806|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 6|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250|organism part:whole organism|rin:10|sample name:E MTAB 13263:Sample 6|scientific name:Danio rerio|sex:na|stimulus:immunosuppression|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 6 p | Sample 6 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2115_dre_C1_clobetasolpropionate_lib667287_10169_3_1.fastq.gz NG-32417_R2115_dre_C1_clobetasolpropionate_lib667287_10169_3_2.fastq.gz | fastq fastq | 10440673634.0 | 34571767.0 | E MTAB 13263:NG 32417 R2115 dre C1 clobetasolpropionate lib667287 10169 3 | 0:151 1:151 | A:2805459166;C:2397120759;G:2463616298;T:2774359989;N:117422 | 151 | 151 | 2805459166 | 2397120759 | 2463616298 | 2774359989 | 117422 | ERX11232845 | ERS16254764 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.95568 | 0.9548 | 0.13056 | 0.12563 | 0.65882 | 0.66332 | 0.49162 | 0.48586 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11831 | 11831 | ERR11834685 | ERX11232838 | ERS16254757 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 10 | SAMEA114265799 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265799|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 10|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250 CP + 4000 IMQ|organism part:whole organism|rin:9.4|sample name:E MTAB 13263:Sample 10|scientific name:Danio rerio|sex:na|stimulus:immunosuppression and immunostimulation|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 10 p | Sample 10 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2119_dre_C1_imq_clobetasolpropionate_lib667291_10169_3_2.fastq.gz NG-32417_R2119_dre_C1_imq_clobetasolpropionate_lib667291_10169_3_1.fastq.gz | fastq fastq | 11267068246.0 | 37308173.0 | E MTAB 13263:NG 32417 R2119 dre C1 imq clobetasolpropionate lib667291 10169 3 | 0:151 1:151 | A:3042432765;C:2574394239;G:2642086000;T:3008026288;N:128954 | 151 | 151 | 3042432765 | 2574394239 | 2642086000 | 3008026288 | 128954 | ERX11232838 | ERS16254757 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.95345 | 0.95411 | 0.13324 | 0.13062 | 0.65796 | 0.65892 | 0.48176 | 0.48174 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 11832 | 11832 | ERR11834686 | ERX11232839 | ERS16254758 | ERP150242 | PRJEB65099 | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E-MTAB-13263 | Transcriptome Analysis | Within the regulatory framework on the approval of new substances the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances clobetasol propionate CP CAS 25122 46 7 and imiquimod IMQ CAS 99011 02 6 on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs ii identify compound specific molecular signatures iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge i.e. the simulation of a resting and an activated immune system. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. RNA quality was assessed with a 2100 Bioanalyzer system… | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | Protocols: At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihyd… | Sample 11 | SAMEA114265800 | Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany | ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265800|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for Molecular Biology and Applied Ecology IME Schmallenberg Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 11|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250 CP + 4000 IMQ|organism part:whole organism|rin:10|sample name:E MTAB 13263:Sample 11|scientific name:Danio rerio|sex:na|stimulus:immunosuppression and immunostimulation|strain:Wildtype AB | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | E MTAB 13263:Sample 11 p | Sample 11 p | Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | At 72 hpf for each sample all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH Germany and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin® Tetra Werke Germany was used as daily main feed regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD 2013. The morning post eggs were collected from the trays using a sieve rinsed with pre tempered system water to remove remaining feces gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy … | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP150242 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression | ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01 | NG-32417_R2120_dre_C1_imq_clobetasolpropionate_lib667292_10169_3_2.fastq.gz NG-32417_R2120_dre_C1_imq_clobetasolpropionate_lib667292_10169_3_1.fastq.gz | fastq fastq | 9922486330.0 | 32855915.0 | E MTAB 13263:NG 32417 R2120 dre C1 imq clobetasolpropionate lib667292 10169 3 | 0:151 1:151 | A:2673462020;C:2268840894;G:2345658284;T:2634411815;N:113317 | 151 | 151 | 2673462020 | 2268840894 | 2345658284 | 2634411815 | 113317 | ERX11232839 | ERS16254758 | ERA26742386 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.9551 | 0.95621 | 0.1193 | 0.11675 | 0.65833 | 0.65827 | 0.48596 | 0.48547 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||||
| 25298 | 25298 | SRR25764100 | SRX21486771 | SRS18719071 | SRP457109 | PRJNA1009810 | Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish | GSE241757 | Transcriptome Analysis | Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells. | pubmed:38265193 | 1 dpf itgb4+ embryonic basal precursors rep2 | GSM7734878 | tissue:epidermal cells|cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing | 1 dpf itgb4+ embryonic basal precursors rep2 | High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values. | epidermal cells | Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY. | The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol. | Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding. | cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry | GSM7734878 | GSM7734878: 1 dpf itgb4+ embryonic basal precursors rep2; Danio rerio; RNA Seq | GSM7734878 r1 | GSM7734878 | 1 | The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-G400 | SRP457109 | itgb4mcherry_2_S229_R1_001.fastq.gz itgb4mcherry_2_S229_R2_001.fastq.gz | fastq fastq | 6040245600.0 | 15100614.0 | GSM7734878 r1 | 0:200 1:200 | A:1588346322;C:1356558310;G:1524614760;T:1569583583;N:1142625 | 200 | 200 | 1588346322 | 1356558310 | 1524614760 | 1569583583 | 1142625 | SRX21486771 | SRS18719071 | SRA1700438 | Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology | Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology | 2 | 0.0156 | 0.0191 | 0.00074 | 0.00093 | 0.99024 | 0.99088 | 0.47058 | 0.47838 | 200 | 200 | T | T | mates < 9% mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2023-08-28 | Multi-stage | Multi-stage | Skin | Surface Structure | ||||||||||
| 25299 | 25299 | SRR25764101 | SRX21486770 | SRS18719070 | SRP457109 | PRJNA1009810 | Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish | GSE241757 | Transcriptome Analysis | Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells. | pubmed:38265193 | 1 dpf itgb4+ embryonic basal precursors rep1 | GSM7734877 | tissue:epidermal cells|cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing | 1 dpf itgb4+ embryonic basal precursors rep1 | High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values. | epidermal cells | Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY. | The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol. | Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding. | cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry | GSM7734877 | GSM7734877: 1 dpf itgb4+ embryonic basal precursors rep1; Danio rerio; RNA Seq | GSM7734877 r1 | GSM7734877 | 1 | The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-G400 | SRP457109 | itgb4mcherry_1_S20_R1_001.fastq.gz itgb4mcherry_1_S20_R2_001.fastq.gz | fastq fastq | 7055215600.0 | 17638039.0 | GSM7734877 r1 | 0:200 1:200 | A:1894635584;C:1556854856;G:1769420212;T:1825520802;N:8784146 | 200 | 200 | 1894635584 | 1556854856 | 1769420212 | 1825520802 | 8784146 | SRX21486770 | SRS18719070 | SRA1700438 | Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology | Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology | 2 | 0.01135 | 0.01881 | 0.00043 | 0.00016 | 0.9932 | 0.99543 | 0.46234 | 0.43106 | 200 | 200 | T | T | mates < 9% mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2023-08-28 | Multi-stage | Multi-stage | Skin | Surface Structure | ||||||||||
| 25300 | 25300 | SRR25764102 | SRX21486769 | SRS18719069 | SRP457109 | PRJNA1009810 | Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish | GSE241757 | Transcriptome Analysis | Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells. | pubmed:38265193 | 1 dpf krt4+ embryonic periderm cells rep2 | GSM7734876 | tissue:epidermal cells|cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp|geo loc name:missing|collection date:missing | 1 dpf krt4+ embryonic periderm cells rep2 | High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values. | epidermal cells | Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY. | The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol. | Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding. | cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp | GSM7734876 | GSM7734876: 1 dpf krt4+ embryonic periderm cells rep2; Danio rerio; RNA Seq | GSM7734876 r1 | GSM7734876 | 1 | The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-G400 | SRP457109 | krt4cre-gfp_2_S4_R2_001.fastq.gz krt4cre-gfp_2_S4_R1_001.fastq.gz | fastq fastq | 9439207600.0 | 23598019.0 | GSM7734876 r1 | 0:200 1:200 | A:2499982675;C:2086665360;G:2395002073;T:2454282285;N:3275207 | 200 | 200 | 2499982675 | 2086665360 | 2395002073 | 2454282285 | 3275207 | SRX21486769 | SRS18719069 | SRA1700438 | Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology | Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology | 2 | 0.44931 | 0.01877 | 0.02236 | 0.00115 | 0.80012 | 0.99032 | 0.45473 | 0.49453 | 200 | 200 | B | T | mate2 technical by mapping diff | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2023-08-28 | Multi-stage | Multi-stage | Skin | Surface Structure | ||||||||||
| 25301 | 25301 | SRR25764103 | SRX21486768 | SRS18719066 | SRP457109 | PRJNA1009810 | Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish | GSE241757 | Transcriptome Analysis | Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells. | pubmed:38265193 | 1 dpf krt4+ embryonic periderm cells rep1 | GSM7734875 | tissue:epidermal cells|cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp|geo loc name:missing|collection date:missing | 1 dpf krt4+ embryonic periderm cells rep1 | High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values. | epidermal cells | Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY. | The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol. | Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding. | cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp | GSM7734875 | GSM7734875: 1 dpf krt4+ embryonic periderm cells rep1; Danio rerio; RNA Seq | GSM7734875 r1 | GSM7734875 | 1 | The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-G400 | SRP457109 | krt4cre-gfp_1_S19_R2_001.fastq.gz krt4cre-gfp_1_S19_R1_001.fastq.gz | fastq fastq | 6119547200.0 | 15298868.0 | GSM7734875 r1 | 0:200 1:200 | A:1642059769;C:1349462427;G:1535937964;T:1584527048;N:7559992 | 200 | 200 | 1642059769 | 1349462427 | 1535937964 | 1584527048 | 7559992 | SRX21486768 | SRS18719066 | SRA1700438 | Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology | Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology | 2 | 0.01112 | 0.01017 | 0.0003 | 0.00014 | 0.9931 | 0.99586 | 0.43605 | 0.40821 | 200 | 200 | T | T | mates < 9% mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2023-08-28 | Multi-stage | Multi-stage | Skin | Surface Structure | ||||||||||
| 26016 | 26016 | SRR25868588 | SRX21589851 | SRS18767424 | SRP457982 | PRJNA1011844 | Comparison of zebrafish toxicity among different developmental windows of exposure to three environmentally relevant PFAS compounds | PRJNA1011844 | Other | The per and polyfluoroalkyl substances PFAS are of significant global concern due to their highly ubiquitous and persistent nature bioaccumulation in organisms and potential toxicity. The aquatic environment is known as an important sink for PFAS resulting in high concentrations in aquatic organisms. However little is known about the developmental windows of sensitivity in which the PFAS chemicals are biologically active in addition to the toxicity endpoints that best reflect chemical hazard. In this study zebrafish Danio rerio were exposed to a 0.33% DMSO vehicle control 1uM chlorpyrifos CAS 2921 88 2 positive control and eight concentrations 0 100 uM half log dilutions of three environmentally relevant PFAS compounds in concentration response: PFOS CAS 1763 21 1 PFOA CAS 45285 51 6 and PFHxS CAS 355 46 4. There was also a group of unexposed zebrafish aliquoted from a single pool into all exposure plates to serve as a quality assurance measure. The goal of this study was to generate transcriptomic point of departure tPOD; a benchmark dose/concentration based treatment level below which a concerted gene expression response is not observed estimates for zebrafish exposed to PFAS compounds as a health protective exposure level for risk assessment. Through the use of short term embryo/larval plate based high throughput toxicity tests tPODs were determined across seven distinct developmental windows 6 hpf 24 hpf 6 hpf 48 hpf 24 hpf 48 hpf 6 hpf 120 hpf 24 hpf 120 hpf 48 hpf 120 hpf 96 hpf 120 hpf to assess how common experimental design variables e.g. different exposure durations exposure at different developmental stages affect point of departure estimates. | T5VAa5 | strain:AB wild type|age:24 hpf 120 hpf|dev stage:embryo|collection date:2022|geo loc name:USA: Minnesota Duluth|sex:not applicable|tissue:whole body zebrafish embryo|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division 6201 Congdon Blvd Duluth MN 55876|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.|collected by:Great Lakes Toxicology & Ecology Division|sample type:Total RNA|time code:5|dose:0|dose units:ug/L|treatment:VehicleControl|replicate ID:rep2|repeat sample:No|BioSampleModel:Model organism or animal | RNA Seq of danio rerio: whole organism embryo control | T5VAa5 S217 | T5VAa5 S217 | At the end of each PFAS exposure period zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol then frozen. RNA was isolated with Ambion MagMAX 96 Total RNA Isolation kit. Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina compatible Lexogen CORALL RNA Seq libraries were then prepared for RNA sequencing. Library pools were quality checked and quantified using a combination of Qubit dsDNA HS Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core. Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis RTA v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP457982 | T5VAa5_S217_L002_R1_001.fastq.gz T5VAa5_S217_L002_R2_001.fastq.gz | fastq fastq | 8100529500.0 | 27001765.0 | T5VAa5 S217 L002 R1 001.fastq.gz | 0:150 1:150 | A:2094646242;C:1839873833;G:2144213073;T:2021734883;N:61469 | 150 | 150 | 2094646242 | 1839873833 | 2144213073 | 2021734883 | 61469 | SRX21589851 | SRS18767424 | SRA1703738 | U.S. Environmental Protection Agency|Great Lakes Toxicology and Ecology Division | U.S. Environmental Protection Agency | 2 | 0.61505 | 0.62102 | 0.08204 | 0.08402 | 0.72581 | 0.72545 | 0.499 | 0.50086 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | lexogen | bulk | unknown | unknown | United States | 2023-09-01 | Multi-stage | Multi-stage | Trunk | Surface Structure | |||||||||||||||||||||
| 29041 | 29041 | SRR26990794 | SRX22683825 | SRS19677539 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | WT gut3 | GSM7924158 | source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing | WT gut3 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | gut | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:gut|genotype:wildtype|time:50dpf | GSM7924158 | GSM7924158: WT gut3; Danio rerio; RNA Seq | GSM7924158 r1 | GSM7924158 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 12_WT_3G_S27_L001_R2_001.fastq.gz 12_WT_3G_S27_L001_R1_001.fastq.gz | fastq fastq | 6066709786.0 | 20088443.0 | GSM7924158 r1 | 0:151 1:151 | A:1673762656;C:1360901090;G:1385125931;T:1646863953;N:56156 | 151 | 151 | 1673762656 | 1360901090 | 1385125931 | 1646863953 | 56156 | SRX22683825 | SRS19677539 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.92515 | 0.9297 | 0.0691 | 0.0659 | 0.75041 | 0.75022 | 0.53007 | 0.53064 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Gut | Digestive System | |||||||||
| 29042 | 29042 | SRR26990795 | SRX22683824 | SRS19677538 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | WT gut2 | GSM7924157 | source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing | WT gut2 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | gut | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:gut|genotype:wildtype|time:50dpf | GSM7924157 | GSM7924157: WT gut2; Danio rerio; RNA Seq | GSM7924157 r1 | GSM7924157 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 11_WT_2G_S26_L001_R2_001.fastq.gz 11_WT_2G_S26_L001_R1_001.fastq.gz | fastq fastq | 5406867570.0 | 17903535.0 | GSM7924157 r1 | 0:151 1:151 | A:1464846243;C:1237183908;G:1259215309;T:1445572498;N:49612 | 151 | 151 | 1464846243 | 1237183908 | 1259215309 | 1445572498 | 49612 | SRX22683824 | SRS19677538 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.93795 | 0.94322 | 0.05952 | 0.05592 | 0.75933 | 0.75887 | 0.54179 | 0.53451 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Gut | Digestive System | |||||||||
| 29043 | 29043 | SRR26990796 | SRX22683823 | SRS19677537 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | WT gut1 | GSM7924156 | source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing | WT gut1 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | gut | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:gut|genotype:wildtype|time:50dpf | GSM7924156 | GSM7924156: WT gut1; Danio rerio; RNA Seq | GSM7924156 r1 | GSM7924156 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 10_WT_1G_S25_L001_R1_001.fastq.gz 10_WT_1G_S25_L001_R2_001.fastq.gz | fastq fastq | 5162192908.0 | 17093354.0 | GSM7924156 r1 | 0:151 1:151 | A:1404682153;C:1175657030;G:1196829496;T:1384975886;N:48343 | 151 | 151 | 1404682153 | 1175657030 | 1196829496 | 1384975886 | 48343 | SRX22683823 | SRS19677537 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.93119 | 0.93585 | 0.06122 | 0.05809 | 0.74757 | 0.74757 | 0.54124 | 0.54417 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Gut | Digestive System | |||||||||
| 29044 | 29044 | SRR26990797 | SRX22683822 | SRS19677536 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | itgavKO gut3 | GSM7924155 | source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing | itgavKO gut3 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | gut | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:gut|genotype:itgavKO mutant|time:50dpf | GSM7924155 | GSM7924155: itgavKO gut3; Danio rerio; RNA Seq | GSM7924155 r1 | GSM7924155 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 9_itgavKO_3G_S24_L001_R2_001.fastq.gz 9_itgavKO_3G_S24_L001_R1_001.fastq.gz | fastq fastq | 4146743578.0 | 13730939.0 | GSM7924155 r1 | 0:151 1:151 | A:1130002132;C:943522869;G:958031732;T:1115146458;N:40387 | 151 | 151 | 1130002132 | 943522869 | 958031732 | 1115146458 | 40387 | SRX22683822 | SRS19677536 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.93764 | 0.94144 | 0.05938 | 0.05594 | 0.7553 | 0.75485 | 0.55535 | 0.55018 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Gut | Digestive System | |||||||||
| 29045 | 29045 | SRR26990798 | SRX22683821 | SRS19677535 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | itgavKO gut2 | GSM7924154 | source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing | itgavKO gut2 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | gut | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:gut|genotype:itgavKO mutant|time:50dpf | GSM7924154 | GSM7924154: itgavKO gut2; Danio rerio; RNA Seq | GSM7924154 r1 | GSM7924154 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 8_itgavKO_2G_S23_L001_R1_001.fastq.gz 8_itgavKO_2G_S23_L001_R2_001.fastq.gz | fastq fastq | 4225756140.0 | 13992570.0 | GSM7924154 r1 | 0:151 1:151 | A:1133211420;C:974497998;G:995876972;T:1122129220;N:40530 | 151 | 151 | 1133211420 | 974497998 | 995876972 | 1122129220 | 40530 | SRX22683821 | SRS19677535 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.95341 | 0.95884 | 0.05109 | 0.04883 | 0.77542 | 0.77368 | 0.51301 | 0.50704 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Gut | Digestive System | |||||||||
| 29046 | 29046 | SRR26990799 | SRX22683820 | SRS19677534 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | itagvKO gut1 | GSM7924153 | source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing | itagvKO gut1 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | gut | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:gut|genotype:itgavKO mutant|time:50dpf | GSM7924153 | GSM7924153: itagvKO gut1; Danio rerio; RNA Seq | GSM7924153 r1 | GSM7924153 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 7_itagvKO_1G_S22_L001_R1_001.fastq.gz 7_itagvKO_1G_S22_L001_R2_001.fastq.gz | fastq fastq | 5954117844.0 | 19715622.0 | GSM7924153 r1 | 0:151 1:151 | A:1600496071;C:1372939932;G:1393534700;T:1587094282;N:52859 | 151 | 151 | 1600496071 | 1372939932 | 1393534700 | 1587094282 | 52859 | SRX22683820 | SRS19677534 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.94807 | 0.95298 | 0.05682 | 0.05385 | 0.74004 | 0.73925 | 0.54423 | 0.54484 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Gut | Digestive System | |||||||||
| 29047 | 29047 | SRR26990800 | SRX22683819 | SRS19677533 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | WT brain 3 | GSM7924152 | source name:brain|tissue:brain|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing | WT brain 3 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | brain | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:brain|genotype:wildtype|time:50dpf | GSM7924152 | GSM7924152: WT brain 3; Danio rerio; RNA Seq | GSM7924152 r1 | GSM7924152 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 6_WT_3B_S21_L001_R2_001.fastq.gz 6_WT_3B_S21_L001_R1_001.fastq.gz | fastq fastq | 4461174200.0 | 14772100.0 | GSM7924152 r1 | 0:151 1:151 | A:1278513355;C:956242646;G:972856171;T:1253520960;N:41068 | 151 | 151 | 1278513355 | 956242646 | 972856171 | 1253520960 | 41068 | SRX22683819 | SRS19677533 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.93808 | 0.93817 | 0.14984 | 0.14408 | 0.70388 | 0.7035 | 0.49899 | 0.49333 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Brain | Nervous System | |||||||||
| 29048 | 29048 | SRR26990801 | SRX22683818 | SRS19677532 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | WT brain 2 | GSM7924151 | source name:brain|tissue:brain|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing | WT brain 2 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | brain | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:brain|genotype:wildtype|time:50dpf | GSM7924151 | GSM7924151: WT brain 2; Danio rerio; RNA Seq | GSM7924151 r1 | GSM7924151 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 5_WT_2B_S20_L001_R2_001.fastq.gz 5_WT_2B_S20_L001_R1_001.fastq.gz | fastq fastq | 4801957946.0 | 15900523.0 | GSM7924151 r1 | 0:151 1:151 | A:1362644269;C:1038749357;G:1059777543;T:1340744881;N:41896 | 151 | 151 | 1362644269 | 1038749357 | 1059777543 | 1340744881 | 41896 | SRX22683818 | SRS19677532 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.9395 | 0.94022 | 0.14136 | 0.13794 | 0.70853 | 0.70845 | 0.48158 | 0.51366 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Brain | Nervous System | |||||||||
| 29049 | 29049 | SRR26990802 | SRX22683817 | SRS19677531 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | WT brain 1 | GSM7924150 | source name:brain|tissue:brain|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing | WT brain 1 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | brain | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:brain|genotype:wildtype|time:50dpf | GSM7924150 | GSM7924150: WT brain 1; Danio rerio; RNA Seq | GSM7924150 r1 | GSM7924150 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 4_WT_1B_S19_L001_R1_001.fastq.gz 4_WT_1B_S19_L001_R2_001.fastq.gz | fastq fastq | 1712568916.0 | 5670758.0 | GSM7924150 r1 | 0:151 1:151 | A:496576572;C:361494257;G:367701092;T:486774148;N:22847 | 151 | 151 | 496576572 | 361494257 | 367701092 | 486774148 | 22847 | SRX22683817 | SRS19677531 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.92654 | 0.92757 | 0.14818 | 0.14172 | 0.71394 | 0.7122 | 0.5011 | 0.50084 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Brain | Nervous System | |||||||||
| 29050 | 29050 | SRR26990803 | SRX22683816 | SRS19677530 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | itgavKO brain 3 | GSM7924149 | source name:brain|tissue:brain|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing | itgavKO brain 3 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | brain | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:brain|genotype:itgavKO mutant|time:50dpf | GSM7924149 | GSM7924149: itgavKO brain 3; Danio rerio; RNA Seq | GSM7924149 r1 | GSM7924149 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 3_itgavKO_3B_S18_L001_R2_001.fastq.gz 3_itgavKO_3B_S18_L001_R1_001.fastq.gz | fastq fastq | 3079420614.0 | 10196757.0 | GSM7924149 r1 | 0:151 1:151 | A:869781292;C:673463468;G:684386550;T:851761331;N:27973 | 151 | 151 | 869781292 | 673463468 | 684386550 | 851761331 | 27973 | SRX22683816 | SRS19677530 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.94057 | 0.94157 | 0.13371 | 0.12847 | 0.70429 | 0.70451 | 0.49726 | 0.49861 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Brain | Nervous System | |||||||||
| 29051 | 29051 | SRR26990804 | SRX22683815 | SRS19677529 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | itgavKO brain 2 | GSM7924148 | source name:brain|tissue:brain|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing | itgavKO brain 2 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | brain | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:brain|genotype:itgavKO mutant|time:50dpf | GSM7924148 | GSM7924148: itgavKO brain 2; Danio rerio; RNA Seq | GSM7924148 r1 | GSM7924148 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 2_itgavKO_2B_S17_L001_R1_001.fastq.gz 2_itgavKO_2B_S17_L001_R2_001.fastq.gz | fastq fastq | 1913701218.0 | 6336759.0 | GSM7924148 r1 | 0:151 1:151 | A:549324781;C:410519448;G:417112515;T:536726028;N:18446 | 151 | 151 | 549324781 | 410519448 | 417112515 | 536726028 | 18446 | SRX22683815 | SRS19677529 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.93075 | 0.93209 | 0.15174 | 0.14613 | 0.70449 | 0.70475 | 0.48199 | 0.48317 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Brain | Nervous System | |||||||||
| 29052 | 29052 | SRR26990805 | SRX22683814 | SRS19677528 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | itgavKO brain 1 | GSM7924147 | source name:brain|tissue:brain|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing | itgavKO brain 1 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | brain | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:brain|genotype:itgavKO mutant|time:50dpf | GSM7924147 | GSM7924147: itgavKO brain 1; Danio rerio; RNA Seq | GSM7924147 r1 | GSM7924147 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 1_itgavKO_1B_S16_L001_R1_001.fastq.gz 1_itgavKO_1B_S16_L001_R2_001.fastq.gz | fastq fastq | 2056389876.0 | 6809238.0 | GSM7924147 r1 | 0:151 1:151 | A:593258034;C:437927433;G:446814957;T:578370581;N:18871 | 151 | 151 | 593258034 | 437927433 | 446814957 | 578370581 | 18871 | SRX22683814 | SRS19677528 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.93156 | 0.93304 | 0.1488 | 0.14352 | 0.70224 | 0.70293 | 0.49609 | 0.49296 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Brain | Nervous System | |||||||||
| 29053 | 29053 | SRR26990806 | SRX22683813 | SRS19677527 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | zebrafish itgavko tc 8d 3 | GSM7924146 | source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf|geo loc name:missing|collection date:missing | zebrafish itgavko tc 8d 3 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | whole fish with tailfin cut | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf | GSM7924146 | GSM7924146: zebrafish itgavko tc 8d 3; Danio rerio; RNA Seq | GSM7924146 r1 | GSM7924146 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 6_zebrafish_itgavko_tc_8d_3_S31_L001_R2_001.fastq.gz 6_zebrafish_itgavko_tc_8d_3_S31_L001_R1_001.fastq.gz | fastq fastq | 3875161320.0 | 12831660.0 | GSM7924146 r1 | 0:151 1:151 | A:1223303253;C:711567515;G:746979670;T:1193309732;N:1150 | 151 | 151 | 1223303253 | 711567515 | 746979670 | 1193309732 | 1150 | SRX22683813 | SRS19677527 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.84595 | 0.84551 | 0.30568 | 0.30506 | 0.77329 | 0.76948 | 0.63885 | 0.64046 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||
| 29054 | 29054 | SRR26990807 | SRX22683812 | SRS19677526 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | zebrafish itgavko tc 8d 2 | GSM7924145 | source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf|geo loc name:missing|collection date:missing | zebrafish itgavko tc 8d 2 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | whole fish with tailfin cut | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf | GSM7924145 | GSM7924145: zebrafish itgavko tc 8d 2; Danio rerio; RNA Seq | GSM7924145 r1 | GSM7924145 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 5_zebrafish_itgavko_tc_8d_2_S30_L001_R1_001.fastq.gz 5_zebrafish_itgavko_tc_8d_2_S30_L001_R2_001.fastq.gz | fastq fastq | 4365991652.0 | 14456926.0 | GSM7924145 r1 | 0:151 1:151 | A:1270600077;C:909032449;G:940039197;T:1246318704;N:1225 | 151 | 151 | 1270600077 | 909032449 | 940039197 | 1246318704 | 1225 | SRX22683812 | SRS19677526 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.91871 | 0.91856 | 0.21085 | 0.20755 | 0.71114 | 0.70873 | 0.45669 | 0.45984 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||
| 29055 | 29055 | SRR26990808 | SRX22683811 | SRS19677525 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | zebrafish itgavko tc 8d 1 | GSM7924144 | source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf|geo loc name:missing|collection date:missing | zebrafish itgavko tc 8d 1 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | whole fish with tailfin cut | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf | GSM7924144 | GSM7924144: zebrafish itgavko tc 8d 1; Danio rerio; RNA Seq | GSM7924144 r1 | GSM7924144 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 4_zebrafish_itgavko_tc_8d_1_S29_L001_R1_001.fastq.gz 4_zebrafish_itgavko_tc_8d_1_S29_L001_R2_001.fastq.gz | fastq fastq | 4802635634.0 | 15902767.0 | GSM7924144 r1 | 0:151 1:151 | A:1431003343;C:965403922;G:1003504713;T:1402722287;N:1369 | 151 | 151 | 1431003343 | 965403922 | 1003504713 | 1402722287 | 1369 | SRX22683811 | SRS19677525 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.90555 | 0.90464 | 0.24806 | 0.24593 | 0.72182 | 0.72007 | 0.46914 | 0.47508 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||
| 29056 | 29056 | SRR26990809 | SRX22683810 | SRS19677524 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | zebrafish wt tc 8d 3 | GSM7924143 | source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:wildtype|time:8dpf|geo loc name:missing|collection date:missing | zebrafish wt tc 8d 3 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | whole fish with tailfin cut | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:whole fish with tailfin cut|genotype:wildtype|time:8dpf | GSM7924143 | GSM7924143: zebrafish wt tc 8d 3; Danio rerio; RNA Seq | GSM7924143 r1 | GSM7924143 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 3_zebrafish_wt_tc_8d_3_S28_L001_R1_001.fastq.gz 3_zebrafish_wt_tc_8d_3_S28_L001_R2_001.fastq.gz | fastq fastq | 4510890648.0 | 14936724.0 | GSM7924143 r1 | 0:151 1:151 | A:1375725383;C:876879135;G:915216593;T:1343068155;N:1382 | 151 | 151 | 1375725383 | 876879135 | 915216593 | 1343068155 | 1382 | SRX22683810 | SRS19677524 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.87519 | 0.87203 | 0.27672 | 0.27432 | 0.74282 | 0.74054 | 0.54199 | 0.54873 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||
| 29057 | 29057 | SRR26990810 | SRX22683809 | SRS19677523 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | zebrafish wt tc 8d 2 | GSM7924142 | source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:wildtype|time:8dpf|geo loc name:missing|collection date:missing | zebrafish wt tc 8d 2 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | whole fish with tailfin cut | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:whole fish with tailfin cut|genotype:wildtype|time:8dpf | GSM7924142 | GSM7924142: zebrafish wt tc 8d 2; Danio rerio; RNA Seq | GSM7924142 r1 | GSM7924142 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 2_zebrafish_wt_tc_8d_2_S27_L001_R1_001.fastq.gz 2_zebrafish_wt_tc_8d_2_S27_L001_R2_001.fastq.gz | fastq fastq | 4596331280.0 | 15219640.0 | GSM7924142 r1 | 0:151 1:151 | A:1337992161;C:955572266;G:991264463;T:1311501025;N:1365 | 151 | 151 | 1337992161 | 955572266 | 991264463 | 1311501025 | 1365 | SRX22683809 | SRS19677523 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.91445 | 0.91384 | 0.21247 | 0.20919 | 0.71135 | 0.70893 | 0.46349 | 0.47487 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||
| 29058 | 29058 | SRR26990811 | SRX22683808 | SRS19677522 | SRP474986 | PRJNA1046526 | ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease | GSE248975 | Transcriptome Analysis | Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency. | pubmed:39526957 | zebrafish wt tc 8d 1 | GSM7924141 | source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:wildtype|time:8dpf|geo loc name:missing|collection date:missing | zebrafish wt tc 8d 1 | The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples. | whole fish with tailfin cut | Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration. | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark. | tissue:whole fish with tailfin cut|genotype:wildtype|time:8dpf | GSM7924141 | GSM7924141: zebrafish wt tc 8d 1; Danio rerio; RNA Seq | GSM7924141 r1 | GSM7924141 | 1 | RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP474986 | loader:fastq load.py | 1_zebrafish_wt_tc_8d_1_S26_L001_R2_001.fastq.gz 1_zebrafish_wt_tc_8d_1_S26_L001_R1_001.fastq.gz | fastq fastq | 3796122786.0 | 12569943.0 | GSM7924141 r1 | 0:151 1:151 | A:1127981217;C:766135618;G:796849753;T:1105155152;N:1046 | 151 | 151 | 1127981217 | 766135618 | 796849753 | 1105155152 | 1046 | SRX22683808 | SRS19677522 | SRA1760061 | Muise Lab, Cell Biology, The Hospital for Sick Children | Muise Lab, Cell Biology, The Hospital for Sick Children | 2 | 0.9074 | 0.90541 | 0.24401 | 0.24217 | 0.7205 | 0.7176 | 0.46736 | 0.47258 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | bulk | unknown | unknown | Canada | 2023-11-29 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||
| 29059 | 29059 | SRR27010032 | SRX22702842 | SRS19695451 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | rnaset2 scr sham C3 | C3 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:C3|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | C3 | C3 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | C3_R2_001.fastq.gz C3_R1_001.fastq.gz | fastq fastq | 7226125500.0 | 24087085.0 | C3 R1 001.fastq.gz | 0:150 1:150 | A:1960622478;C:1648410555;G:1694156766;T:1922924543;N:11158 | 150 | 150 | 1960622478 | 1648410555 | 1694156766 | 1922924543 | 11158 | SRX22702842 | SRS19695451 | SRA1760882 | University of York|Biology | University of York | 2 | 0.94281 | 0.94259 | 0.11548 | 0.11243 | 0.666 | 0.66768 | 0.4931 | 0.49197 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29060 | 29060 | SRR27010033 | SRX22702841 | SRS19695450 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | rnaset2 scr sham C2 | C2 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:C2|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | C2 | C2 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | C2_R1_001.fastq.gz C2_R2_001.fastq.gz | fastq fastq | 5174981700.0 | 17249939.0 | C2 R1 001.fastq.gz | 0:150 1:150 | A:1397754308;C:1184093732;G:1220417954;T:1372707855;N:7851 | 150 | 150 | 1397754308 | 1184093732 | 1220417954 | 1372707855 | 7851 | SRX22702841 | SRS19695450 | SRA1760882 | University of York|Biology | University of York | 2 | 0.94447 | 0.94375 | 0.11969 | 0.11666 | 0.68885 | 0.68956 | 0.49127 | 0.48884 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29061 | 29061 | SRR27010034 | SRX22702840 | SRS19695449 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | WT irf8 sham B6 | B6 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:B6|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | B6 | B6 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | B6_R1_001.fastq.gz B6_R2_001.fastq.gz | fastq fastq | 6038798100.0 | 20129327.0 | B6 R1 001.fastq.gz | 0:150 1:150 | A:1644314055;C:1369774666;G:1410590989;T:1614109292;N:9098 | 150 | 150 | 1644314055 | 1369774666 | 1410590989 | 1614109292 | 9098 | SRX22702840 | SRS19695449 | SRA1760882 | University of York|Biology | University of York | 2 | 0.94338 | 0.9424 | 0.12398 | 0.12103 | 0.69075 | 0.69203 | 0.49627 | 0.49707 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29062 | 29062 | SRR27010035 | SRX22702839 | SRS19695448 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | WT irf8 sham B4 | B4 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:B4|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | B4 | B4 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | B4_R1_001.fastq.gz B4_R2_001.fastq.gz | fastq fastq | 4670850600.0 | 15569502.0 | B4 R1 001.fastq.gz | 0:150 1:150 | A:1265811314;C:1065724201;G:1097798356;T:1241510089;N:6640 | 150 | 150 | 1265811314 | 1065724201 | 1097798356 | 1241510089 | 6640 | SRX22702839 | SRS19695448 | SRA1760882 | University of York|Biology | University of York | 2 | 0.94547 | 0.94517 | 0.11922 | 0.11549 | 0.68968 | 0.69029 | 0.48585 | 0.48669 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29063 | 29063 | SRR27010036 | SRX22702838 | SRS19695446 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | WT irf8 sham B3 | B3 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:B3|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | B3 | B3 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | B3_R1_001.fastq.gz B3_R2_001.fastq.gz | fastq fastq | 5982538500.0 | 19941795.0 | B3 R1 001.fastq.gz | 0:150 1:150 | A:1606272011;C:1379162914;G:1419047430;T:1578047050;N:9095 | 150 | 150 | 1606272011 | 1379162914 | 1419047430 | 1578047050 | 9095 | SRX22702838 | SRS19695446 | SRA1760882 | University of York|Biology | University of York | 2 | 0.95017 | 0.9501 | 0.09939 | 0.09688 | 0.68838 | 0.68964 | 0.48756 | 0.49223 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29064 | 29064 | SRR27010037 | SRX22702837 | SRS19695447 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | WT irf8 sham B2 | B2 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:B2|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | B2 | B2 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | B2_R2_001.fastq.gz B2_R1_001.fastq.gz | fastq fastq | 5653227300.0 | 18844091.0 | B2 R1 001.fastq.gz | 0:150 1:150 | A:1525579353;C:1295599509;G:1332714404;T:1499325712;N:8322 | 150 | 150 | 1525579353 | 1295599509 | 1332714404 | 1499325712 | 8322 | SRX22702837 | SRS19695447 | SRA1760882 | University of York|Biology | University of York | 2 | 0.94379 | 0.89488 | 0.12085 | 0.10989 | 0.69004 | 0.69796 | 0.48877 | 0.48916 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29065 | 29065 | SRR27010038 | SRX22702836 | SRS19695445 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | WT scr sham A9 | A9 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:A9|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | A9 | A9 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | A9_R1_001.fastq.gz A9_R2_001.fastq.gz | fastq fastq | 5280286800.0 | 17600956.0 | A9 R1 001.fastq.gz | 0:150 1:150 | A:1438789477;C:1200820278;G:1228527888;T:1412141110;N:8047 | 150 | 150 | 1438789477 | 1200820278 | 1228527888 | 1412141110 | 8047 | SRX22702836 | SRS19695445 | SRA1760882 | University of York|Biology | University of York | 2 | 0.93991 | 0.93997 | 0.12415 | 0.11988 | 0.68043 | 0.68245 | 0.49031 | 0.49263 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29066 | 29066 | SRR27010039 | SRX22702835 | SRS19695444 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | rnaset2 irf8 transplanted visible cells G8 | G8 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:G8|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | G8 | G8 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | G8_R1_001.fastq.gz G8_R2_001.fastq.gz | fastq fastq | 6258269400.0 | 20860898.0 | G8 R1 001.fastq.gz | 0:150 1:150 | A:1703536007;C:1424705894;G:1461517358;T:1668500971;N:9170 | 150 | 150 | 1703536007 | 1424705894 | 1461517358 | 1668500971 | 9170 | SRX22702835 | SRS19695444 | SRA1760882 | University of York|Biology | University of York | 2 | 0.94463 | 0.94425 | 0.12179 | 0.11924 | 0.68383 | 0.68574 | 0.48927 | 0.49078 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29067 | 29067 | SRR27010040 | SRX22702834 | SRS19695443 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | rnaset2 irf8 transplanted visible cells G5 | G5 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:G5|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | G5 | G5 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | G5_R2_001.fastq.gz G5_R1_001.fastq.gz | fastq fastq | 8086012500.0 | 26953375.0 | G5 R1 001.fastq.gz | 0:150 1:150 | A:2209424775;C:1827141351;G:1886144200;T:2163290263;N:11911 | 150 | 150 | 2209424775 | 1827141351 | 1886144200 | 2163290263 | 11911 | SRX22702834 | SRS19695443 | SRA1760882 | University of York|Biology | University of York | 2 | 0.94005 | 0.94009 | 0.13869 | 0.13535 | 0.68874 | 0.68876 | 0.49518 | 0.49562 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29068 | 29068 | SRR27010041 | SRX22702833 | SRS19695442 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | rnaset2 irf8 transplanted visible cells G4 | G4 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:G4|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | G4 | G4 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | G4_R2_001.fastq.gz G4_R1_001.fastq.gz | fastq fastq | 11168836800.0 | 37229456.0 | G4 R1 001.fastq.gz | 0:150 1:150 | A:3056935929;C:2522420915;G:2603785258;T:2985677785;N:16913 | 150 | 150 | 3056935929 | 2522420915 | 2603785258 | 2985677785 | 16913 | SRX22702833 | SRS19695442 | SRA1760882 | University of York|Biology | University of York | 2 | 0.94154 | 0.94245 | 0.13303 | 0.12991 | 0.68298 | 0.68428 | 0.49109 | 0.49258 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29069 | 29069 | SRR27010042 | SRX22702832 | SRS19695441 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | rnaset2 irf8 transplanted visible cells G1 | G1 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:G1|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | G1 | G1 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | G1_R1_001.fastq.gz G1_R2_001.fastq.gz | fastq fastq | 6745303500.0 | 22484345.0 | G1 R1 001.fastq.gz | 0:150 1:150 | A:1832990297;C:1535916761;G:1572331210;T:1804054965;N:10267 | 150 | 150 | 1832990297 | 1535916761 | 1572331210 | 1804054965 | 10267 | SRX22702832 | SRS19695441 | SRA1760882 | University of York|Biology | University of York | 2 | 0.9424 | 0.94298 | 0.12822 | 0.12534 | 0.68775 | 0.68854 | 0.4869 | 0.48958 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29070 | 29070 | SRR27010043 | SRX22702831 | SRS19695440 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | rnaset2 scr transplanted non visible cells F5 | F5 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:F5|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | F5 | F5 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | F5_R1_001.fastq.gz F5_R2_001.fastq.gz | fastq fastq | 6464113800.0 | 21547046.0 | F5 R1 001.fastq.gz | 0:150 1:150 | A:1773652408;C:1452872569;G:1501709404;T:1735869784;N:9635 | 150 | 150 | 1773652408 | 1452872569 | 1501709404 | 1735869784 | 9635 | SRX22702831 | SRS19695440 | SRA1760882 | University of York|Biology | University of York | 2 | 0.93953 | 0.93885 | 0.13889 | 0.13589 | 0.68448 | 0.68568 | 0.49419 | 0.49486 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29071 | 29071 | SRR27010044 | SRX22702830 | SRS19695439 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | rnaset2 scr transplanted non visible cells F4 | F4 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:F4|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | F4 | F4 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | F4_R1_001.fastq.gz F4_R2_001.fastq.gz | fastq fastq | 7547491800.0 | 25158306.0 | F4 R1 001.fastq.gz | 0:150 1:150 | A:2043215956;C:1726123019;G:1778767478;T:1999373636;N:11711 | 150 | 150 | 2043215956 | 1726123019 | 1778767478 | 1999373636 | 11711 | SRX22702830 | SRS19695439 | SRA1760882 | University of York|Biology | University of York | 2 | 0.94829 | 0.94765 | 0.11775 | 0.11477 | 0.68682 | 0.68783 | 0.48624 | 0.49294 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29072 | 29072 | SRR27010045 | SRX22702829 | SRS19695437 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | rnaset2 scr transplanted non visible cells F3 | F3 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:F3|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | F3 | F3 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | F3_R1_001.fastq.gz F3_R2_001.fastq.gz | fastq fastq | 7796779800.0 | 25989266.0 | F3 R1 001.fastq.gz | 0:150 1:150 | A:2138759764;C:1759352855;G:1808448742;T:2090206548;N:11891 | 150 | 150 | 2138759764 | 1759352855 | 1808448742 | 2090206548 | 11891 | SRX22702829 | SRS19695437 | SRA1760882 | University of York|Biology | University of York | 2 | 0.94125 | 0.9421 | 0.13575 | 0.13224 | 0.69307 | 0.69469 | 0.4862 | 0.48802 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29073 | 29073 | SRR27010046 | SRX22702828 | SRS19695438 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | WT scr sham A4 | A4 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:A4|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | A4 | A4 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | A4_R1_001.fastq.gz A4_R2_001.fastq.gz | fastq fastq | 6954570300.0 | 23181901.0 | A4 R1 001.fastq.gz | 0:150 1:150 | A:1888329109;C:1587042583;G:1627429667;T:1851758485;N:10456 | 150 | 150 | 1888329109 | 1587042583 | 1627429667 | 1851758485 | 10456 | SRX22702828 | SRS19695438 | SRA1760882 | University of York|Biology | University of York | 2 | 0.94568 | 0.94593 | 0.11814 | 0.1154 | 0.69171 | 0.69161 | 0.49417 | 0.49201 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29074 | 29074 | SRR27010047 | SRX22702827 | SRS19695436 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | rnaset2 scr transplanted non visible cells F2 | F2 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:F2|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | F2 | F2 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | F2_R2_001.fastq.gz F2_R1_001.fastq.gz | fastq fastq | 7064875200.0 | 23549584.0 | F2 R1 001.fastq.gz | 0:150 1:150 | A:1909747576;C:1617295332;G:1667877510;T:1869944260;N:10522 | 150 | 150 | 1909747576 | 1617295332 | 1667877510 | 1869944260 | 10522 | SRX22702827 | SRS19695436 | SRA1760882 | University of York|Biology | University of York | 2 | 0.94737 | 0.94827 | 0.10024 | 0.09772 | 0.69057 | 0.69146 | 0.49402 | 0.49924 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29075 | 29075 | SRR27010048 | SRX22702826 | SRS19695435 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | rnaset2 scr transplanted visible cells E5 | E5 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:E5|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | E5 | E5 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | E5_R1_001.fastq.gz E5_R2_001.fastq.gz | fastq fastq | 9245045700.0 | 30816819.0 | E5 R1 001.fastq.gz | 0:150 1:150 | A:2541240585;C:2078884464;G:2136224399;T:2488682323;N:13929 | 150 | 150 | 2541240585 | 2078884464 | 2136224399 | 2488682323 | 13929 | SRX22702826 | SRS19695435 | SRA1760882 | University of York|Biology | University of York | 2 | 0.93981 | 0.93963 | 0.14018 | 0.13679 | 0.68544 | 0.68647 | 0.48749 | 0.49123 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29076 | 29076 | SRR27010049 | SRX22702825 | SRS19695434 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | rnaset2 scr transplanted visible cells E4 | E4 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:E4|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | E4 | E4 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | E4_R1_001.fastq.gz E4_R2_001.fastq.gz | fastq fastq | 9413066700.0 | 31376889.0 | E4 R1 001.fastq.gz | 0:150 1:150 | A:2556541599;C:2141951710;G:2209637678;T:2504921319;N:14394 | 150 | 150 | 2556541599 | 2141951710 | 2209637678 | 2504921319 | 14394 | SRX22702825 | SRS19695434 | SRA1760882 | University of York|Biology | University of York | 2 | 0.93966 | 0.94056 | 0.13191 | 0.13025 | 0.6845 | 0.68458 | 0.48562 | 0.48775 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29077 | 29077 | SRR27010050 | SRX22702824 | SRS19695433 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | rnaset2 scr transplanted visible cells E3 | E3 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:E3|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | E3 | E3 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | E3_R1_001.fastq.gz E3_R2_001.fastq.gz | fastq fastq | 7964919000.0 | 26549730.0 | E3 R1 001.fastq.gz | 0:150 1:150 | A:2160541660;C:1817481684;G:1869600595;T:2117282750;N:12311 | 150 | 150 | 2160541660 | 1817481684 | 1869600595 | 2117282750 | 12311 | SRX22702824 | SRS19695433 | SRA1760882 | University of York|Biology | University of York | 2 | 0.94418 | 0.94436 | 0.12381 | 0.12155 | 0.69043 | 0.69244 | 0.49578 | 0.49427 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29078 | 29078 | SRR27010051 | SRX22702823 | SRS19695432 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | rnaset2 irf8 sham D7 | D7 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:D7|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | D7 | D7 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | D7_R1_001.fastq.gz D7_R2_001.fastq.gz | fastq fastq | 9187165200.0 | 30623884.0 | D7 R1 001.fastq.gz | 0:150 1:150 | A:2491532789;C:2097618431;G:2151100077;T:2446900236;N:13667 | 150 | 150 | 2491532789 | 2097618431 | 2151100077 | 2446900236 | 13667 | SRX22702823 | SRS19695432 | SRA1760882 | University of York|Biology | University of York | 2 | 0.94299 | 0.94212 | 0.11906 | 0.11545 | 0.68306 | 0.68548 | 0.49177 | 0.49121 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29079 | 29079 | SRR27010052 | SRX22702822 | SRS19695430 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | rnaset2 irf8 sham D6 | D6 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:D6|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | D6 | D6 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | D6_R1_001.fastq.gz D6_R2_001.fastq.gz | fastq fastq | 5879800500.0 | 19599335.0 | D6 R1 001.fastq.gz | 0:150 1:150 | A:1605109827;C:1329412433;G:1368575434;T:1576693845;N:8961 | 150 | 150 | 1605109827 | 1329412433 | 1368575434 | 1576693845 | 8961 | SRX22702822 | SRS19695430 | SRA1760882 | University of York|Biology | University of York | 2 | 0.94062 | 0.94076 | 0.12643 | 0.12267 | 0.67959 | 0.68079 | 0.4953 | 0.49028 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29080 | 29080 | SRR27010053 | SRX22702821 | SRS19695431 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | rnaset2 irf8 sham D5 | D5 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:D5|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | D5 | D5 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | D5_R1_001.fastq.gz D5_R2_001.fastq.gz | fastq fastq | 6561881400.0 | 21872938.0 | D5 R1 001.fastq.gz | 0:150 1:150 | A:1784761040;C:1494553700;G:1531680450;T:1750875924;N:10286 | 150 | 150 | 1784761040 | 1494553700 | 1531680450 | 1750875924 | 10286 | SRX22702821 | SRS19695431 | SRA1760882 | University of York|Biology | University of York | 2 | 0.94309 | 0.94372 | 0.12249 | 0.11939 | 0.6896 | 0.69126 | 0.4916 | 0.48496 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29081 | 29081 | SRR27010054 | SRX22702820 | SRS19695429 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | rnaset2 irf8 sham D2 | D2 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:D2|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | D2 | D2 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | D2_R1_001.fastq.gz D2_R2_001.fastq.gz | fastq fastq | 6654501900.0 | 22181673.0 | D2 R1 001.fastq.gz | 0:150 1:150 | A:1814773421;C:1511191953;G:1552895235;T:1775631113;N:10178 | 150 | 150 | 1814773421 | 1511191953 | 1552895235 | 1775631113 | 10178 | SRX22702820 | SRS19695429 | SRA1760882 | University of York|Biology | University of York | 2 | 0.94117 | 0.94183 | 0.13042 | 0.12757 | 0.68578 | 0.68747 | 0.49634 | 0.49724 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29082 | 29082 | SRR27010055 | SRX22702819 | SRS19695428 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | rnaset2 scr sham C5 | C5 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:C5|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | C5 | C5 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | C5_R2_001.fastq.gz C5_R1_001.fastq.gz | fastq fastq | 6839917500.0 | 22799725.0 | C5 R1 001.fastq.gz | 0:150 1:150 | A:1862202751;C:1544536021;G:1599909841;T:1833258970;N:9917 | 150 | 150 | 1862202751 | 1544536021 | 1599909841 | 1833258970 | 9917 | SRX22702819 | SRS19695428 | SRA1760882 | University of York|Biology | University of York | 2 | 0.94311 | 0.9429 | 0.12484 | 0.12074 | 0.68899 | 0.69077 | 0.49108 | 0.49366 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29083 | 29083 | SRR27010056 | SRX22702818 | SRS19695427 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | rnaset2 scr sham C4 | C4 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:C4|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | C4 | C4 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | C4_R1_001.fastq.gz C4_R2_001.fastq.gz | fastq fastq | 6814278600.0 | 22714262.0 | C4 R1 001.fastq.gz | 0:150 1:150 | A:1829280895;C:1574717969;G:1616401528;T:1793867756;N:10452 | 150 | 150 | 1829280895 | 1574717969 | 1616401528 | 1793867756 | 10452 | SRX22702818 | SRS19695427 | SRA1760882 | University of York|Biology | University of York | 2 | 0.94942 | 0.95087 | 0.09719 | 0.09395 | 0.69445 | 0.69507 | 0.49061 | 0.49227 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29084 | 29084 | SRR27010057 | SRX22702817 | SRS19695425 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | WT scr sham A2 | A2 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:A2|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | A2 | A2 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | A2_R1_001.fastq.gz A2_R2_001.fastq.gz | fastq fastq | 9528853800.0 | 31762846.0 | A2 R1 001.fastq.gz | 0:150 1:150 | A:2597197507;C:2160049241;G:2216864264;T:2554728048;N:14740 | 150 | 150 | 2597197507 | 2160049241 | 2216864264 | 2554728048 | 14740 | SRX22702817 | SRS19695425 | SRA1760882 | University of York|Biology | University of York | 2 | 0.9445 | 0.94377 | 0.12789 | 0.12443 | 0.68414 | 0.68456 | 0.48493 | 0.49203 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29085 | 29085 | SRR27010058 | SRX22702816 | SRS19695426 | SRP475263 | PRJNA1047321 | Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish | PRJNA1047321 | Other | RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy. | WT scr sham A1 | A1 | strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:A1|BioSampleModel:Model organism or animal | RNA seq of zebrafish: brain | A1 | A1 | RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475263 | A1_R1_001.fastq.gz A1_R2_001.fastq.gz | fastq fastq | 7478013000.0 | 24926710.0 | A1 R1 001.fastq.gz | 0:150 1:150 | A:2052485809;C:1681219485;G:1732402686;T:2011893634;N:11386 | 150 | 150 | 2052485809 | 1681219485 | 1732402686 | 2011893634 | 11386 | SRX22702816 | SRS19695426 | SRA1760882 | University of York|Biology | University of York | 2 | 0.9395 | 0.93867 | 0.13153 | 0.12753 | 0.68933 | 0.691 | 0.4882 | 0.48774 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-01 | Multi-stage | Multi-stage | Brain | Nervous System | ||||||||||||||||||||
| 29175 | 29175 | SRR27292304 | SRX22969963 | SRS19936063 | SRP479046 | PRJNA1054617 | Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish | GSE250610 | Transcriptome Analysis | Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de… | pubmed:38922186 | Burned Larval Zebrafish 48 hours post burn | GSM7982886 | source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing | Burned Larval Zebrafish 48 hours post burn | FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix | Whole blood | Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. | tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn | GSM7982886 | GSM7982886: Burned Larval Zebrafish 48 hours post burn; Danio rerio; RNA Seq | GSM7982886 r1 | GSM7982886 | 1 | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP479046 | loader:fastq load.py | Burn-48hpb_S5_L001_R2_001.fastq.gz Burn-48hpb_S5_L001_R1_001.fastq.gz | fastq fastq | 20874980529.0 | 178418637.0 | GSM7982886 r1 | 0:28 1:89 | A:5945091269;C:4392590896;G:4497688824;T:6035946283;N:3663257 | 28 | 89 | 5945091269 | 4392590896 | 4497688824 | 6035946283 | 3663257 | SRX22969963 | SRS19936063 | SRA1772557 | University of Wisconsin-Madison | University of Wisconsin-Madison | 2 | 0.00573 | 0.91666 | 0.00222 | 0.19474 | 0.9931 | 0.79306 | 0.42082 | 0.53801 | 28 | 89 | T | B | sc-like readlen | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United States | 2023-12-19 | Multi-stage | Multi-stage | Blood | Hematopoietic System | |||||||||
| 29176 | 29176 | SRR27292305 | SRX22969963 | SRS19936063 | SRP479046 | PRJNA1054617 | Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish | GSE250610 | Transcriptome Analysis | Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de… | pubmed:38922186 | Burned Larval Zebrafish 48 hours post burn | GSM7982886 | source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing | Burned Larval Zebrafish 48 hours post burn | FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix | Whole blood | Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. | tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn | GSM7982886 | GSM7982886: Burned Larval Zebrafish 48 hours post burn; Danio rerio; RNA Seq | GSM7982886 r1 | GSM7982886 | 1 | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP479046 | loader:fastq load.py | Burn-48hpb_S5_L002_R1_001.fastq.gz Burn-48hpb_S5_L002_R2_001.fastq.gz | fastq fastq | 20022973425.0 | 171136525.0 | GSM7982886 r2 | 0:28 1:89 | A:5709681181;C:4208386174;G:4307510275;T:5796282368;N:1113427 | 28 | 89 | 5709681181 | 4208386174 | 4307510275 | 5796282368 | 1113427 | SRX22969963 | SRS19936063 | SRA1772557 | University of Wisconsin-Madison | University of Wisconsin-Madison | 2 | 0.00547 | 0.9154 | 0.00202 | 0.1955 | 0.99283 | 0.79423 | 0.39307 | 0.53427 | 28 | 89 | T | B | sc-like readlen | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United States | 2023-12-19 | Multi-stage | Multi-stage | Blood | Hematopoietic System | |||||||||
| 29177 | 29177 | SRR27292306 | SRX22969962 | SRS19936064 | SRP479046 | PRJNA1054617 | Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish | GSE250610 | Transcriptome Analysis | Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de… | pubmed:38922186 | Burned Larval Zebrafish 24 hours post burn | GSM7982885 | source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing | Burned Larval Zebrafish 24 hours post burn | FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix | Whole blood | Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. | tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn | GSM7982885 | GSM7982885: Burned Larval Zebrafish 24 hours post burn; Danio rerio; RNA Seq | GSM7982885 r1 | GSM7982885 | 1 | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP479046 | loader:fastq load.py | Burn-24hpb_S2_L001_R1_001.fastq.gz Burn-24hpb_S2_L001_R2_001.fastq.gz | fastq fastq | 9782870058.0 | 83614274.0 | GSM7982885 r1 | 0:28 1:89 | A:2744737668;C:2140848416;G:2249400157;T:2645170677;N:2713140 | 28 | 89 | 2744737668 | 2140848416 | 2249400157 | 2645170677 | 2713140 | SRX22969962 | SRS19936064 | SRA1772557 | University of Wisconsin-Madison | University of Wisconsin-Madison | 2 | 0.00752 | 0.92059 | 0.00244 | 0.16143 | 0.98944 | 0.82929 | 0.44176 | 0.54525 | 28 | 89 | T | B | sc-like readlen | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United States | 2023-12-19 | Multi-stage | Multi-stage | Blood | Hematopoietic System | |||||||||
| 29178 | 29178 | SRR27292307 | SRX22969962 | SRS19936064 | SRP479046 | PRJNA1054617 | Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish | GSE250610 | Transcriptome Analysis | Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de… | pubmed:38922186 | Burned Larval Zebrafish 24 hours post burn | GSM7982885 | source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing | Burned Larval Zebrafish 24 hours post burn | FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix | Whole blood | Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. | tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn | GSM7982885 | GSM7982885: Burned Larval Zebrafish 24 hours post burn; Danio rerio; RNA Seq | GSM7982885 r1 | GSM7982885 | 1 | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP479046 | loader:fastq load.py | Burn-24hpb_S2_L002_R2_001.fastq.gz Burn-24hpb_S2_L002_R1_001.fastq.gz | fastq fastq | 9861989202.0 | 84290506.0 | GSM7982885 r2 | 0:28 1:89 | A:2769268861;C:2158644227;G:2263475493;T:2669311436;N:1289185 | 28 | 89 | 2769268861 | 2158644227 | 2263475493 | 2669311436 | 1289185 | SRX22969962 | SRS19936064 | SRA1772557 | University of Wisconsin-Madison | University of Wisconsin-Madison | 2 | 0.0076 | 0.9197 | 0.00232 | 0.16162 | 0.98995 | 0.82852 | 0.43786 | 0.55256 | 28 | 89 | T | B | sc-like readlen | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United States | 2023-12-19 | Multi-stage | Multi-stage | Blood | Hematopoietic System | |||||||||
| 29179 | 29179 | SRR27292308 | SRX22969961 | SRS19936062 | SRP479046 | PRJNA1054617 | Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish | GSE250610 | Transcriptome Analysis | Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de… | pubmed:38922186 | Burned Larval Zebrafish 6 hours post burn | GSM7982884 | source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing | Burned Larval Zebrafish 6 hours post burn | FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix | Whole blood | Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. | tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn | GSM7982884 | GSM7982884: Burned Larval Zebrafish 6 hours post burn; Danio rerio; RNA Seq | GSM7982884 r1 | GSM7982884 | 1 | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP479046 | loader:fastq load.py | Burn-6hpb_S7_L001_R1_001.fastq.gz Burn-6hpb_S7_L001_R2_001.fastq.gz | fastq fastq | 12475938384.0 | 106631952.0 | GSM7982884 r1 | 0:28 1:89 | A:3401989108;C:2878275107;G:3114945415;T:3078525361;N:2203393 | 28 | 89 | 3401989108 | 2878275107 | 3114945415 | 3078525361 | 2203393 | SRX22969961 | SRS19936062 | SRA1772557 | University of Wisconsin-Madison | University of Wisconsin-Madison | 2 | 0.01053 | 0.89396 | 0.00429 | 0.18315 | 0.99458 | 0.85756 | 0.34876 | 0.58728 | 28 | 89 | T | B | sc-like readlen | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United States | 2023-12-19 | Multi-stage | Multi-stage | Blood | Hematopoietic System | |||||||||
| 29180 | 29180 | SRR27292309 | SRX22969961 | SRS19936062 | SRP479046 | PRJNA1054617 | Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish | GSE250610 | Transcriptome Analysis | Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de… | pubmed:38922186 | Burned Larval Zebrafish 6 hours post burn | GSM7982884 | source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing | Burned Larval Zebrafish 6 hours post burn | FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix | Whole blood | Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. | tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn | GSM7982884 | GSM7982884: Burned Larval Zebrafish 6 hours post burn; Danio rerio; RNA Seq | GSM7982884 r1 | GSM7982884 | 1 | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP479046 | loader:fastq load.py | Burn-6hpb_S7_L002_R1_001.fastq.gz Burn-6hpb_S7_L002_R2_001.fastq.gz | fastq fastq | 11874083247.0 | 101487891.0 | GSM7982884 r2 | 0:28 1:89 | A:3243501055;C:2735412615;G:2958387721;T:2936117380;N:664476 | 28 | 89 | 3243501055 | 2735412615 | 2958387721 | 2936117380 | 664476 | SRX22969961 | SRS19936062 | SRA1772557 | University of Wisconsin-Madison | University of Wisconsin-Madison | 2 | 0.01063 | 0.89389 | 0.00439 | 0.18047 | 0.99403 | 0.85878 | 0.36393 | 0.54831 | 28 | 89 | T | B | sc-like readlen | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United States | 2023-12-19 | Multi-stage | Multi-stage | Blood | Hematopoietic System | |||||||||
| 29181 | 29181 | SRR27292310 | SRX22969960 | SRS19936061 | SRP479046 | PRJNA1054617 | Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish | GSE250610 | Transcriptome Analysis | Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de… | pubmed:38922186 | Unwounded Larval Zebrafish 5 dpf | GSM7982883 | source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing | Unwounded Larval Zebrafish 5 dpf | FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix | Whole blood | Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. | tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded | GSM7982883 | GSM7982883: Unwounded Larval Zebrafish 5 dpf Danio rerio; RNA Seq | GSM7982883 r1 | GSM7982883 | 1 | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP479046 | loader:fastq load.py | WT-5dpf_S6_L001_R2_001.fastq.gz WT-5dpf_S6_L001_R1_001.fastq.gz | fastq fastq | 31813158312.0 | 271907336.0 | GSM7982883 r1 | 0:28 1:89 | A:8991313503;C:6911976524;G:7105775004;T:8798521232;N:5572049 | 28 | 89 | 8991313503 | 6911976524 | 7105775004 | 8798521232 | 5572049 | SRX22969960 | SRS19936061 | SRA1772557 | University of Wisconsin-Madison | University of Wisconsin-Madison | 2 | 0.00661 | 0.92343 | 0.00245 | 0.19293 | 0.99255 | 0.81379 | 0.35935 | 0.54818 | 28 | 89 | T | B | sc-like readlen | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United States | 2023-12-19 | Multi-stage | Multi-stage | Blood | Hematopoietic System | |||||||||
| 29182 | 29182 | SRR27292311 | SRX22969960 | SRS19936061 | SRP479046 | PRJNA1054617 | Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish | GSE250610 | Transcriptome Analysis | Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de… | pubmed:38922186 | Unwounded Larval Zebrafish 5 dpf | GSM7982883 | source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing | Unwounded Larval Zebrafish 5 dpf | FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix | Whole blood | Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. | tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded | GSM7982883 | GSM7982883: Unwounded Larval Zebrafish 5 dpf Danio rerio; RNA Seq | GSM7982883 r1 | GSM7982883 | 1 | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP479046 | loader:fastq load.py | WT-5dpf_S6_L002_R1_001.fastq.gz WT-5dpf_S6_L002_R2_001.fastq.gz | fastq fastq | 30524386113.0 | 260892189.0 | GSM7982883 r2 | 0:28 1:89 | A:8637605077;C:6625244702;G:6807369409;T:8452468968;N:1697957 | 28 | 89 | 8637605077 | 6625244702 | 6807369409 | 8452468968 | 1697957 | SRX22969960 | SRS19936061 | SRA1772557 | University of Wisconsin-Madison | University of Wisconsin-Madison | 2 | 0.00648 | 0.92418 | 0.00233 | 0.19549 | 0.99241 | 0.81444 | 0.37733 | 0.54674 | 28 | 89 | T | B | sc-like readlen | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United States | 2023-12-19 | Multi-stage | Multi-stage | Blood | Hematopoietic System | |||||||||
| 29183 | 29183 | SRR27292312 | SRX22969959 | SRS19936060 | SRP479046 | PRJNA1054617 | Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish | GSE250610 | Transcriptome Analysis | Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de… | pubmed:38922186 | Unwounded Larval Zebrafish 4 dpf | GSM7982882 | source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing | Unwounded Larval Zebrafish 4 dpf | FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix | Whole blood | Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. | tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded | GSM7982882 | GSM7982882: Unwounded Larval Zebrafish 4 dpf Danio rerio; RNA Seq | GSM7982882 r1 | GSM7982882 | 1 | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP479046 | loader:fastq load.py | WT-4dpf_S1_L001_R1_001.fastq.gz WT-4dpf_S1_L001_R2_001.fastq.gz | fastq fastq | 12682286721.0 | 108395613.0 | GSM7982882 r1 | 0:28 1:89 | A:3575375325;C:2777398557;G:2900088646;T:3425909511;N:3514682 | 28 | 89 | 3575375325 | 2777398557 | 2900088646 | 3425909511 | 3514682 | SRX22969959 | SRS19936060 | SRA1772557 | University of Wisconsin-Madison | University of Wisconsin-Madison | 2 | 0.00505 | 0.92112 | 0.00185 | 0.16865 | 0.99257 | 0.8258 | 0.38216 | 0.5512 | 28 | 89 | T | B | sc-like readlen | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United States | 2023-12-19 | Multi-stage | Multi-stage | Blood | Hematopoietic System | |||||||||
| 29184 | 29184 | SRR27292313 | SRX22969959 | SRS19936060 | SRP479046 | PRJNA1054617 | Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish | GSE250610 | Transcriptome Analysis | Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de… | pubmed:38922186 | Unwounded Larval Zebrafish 4 dpf | GSM7982882 | source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing | Unwounded Larval Zebrafish 4 dpf | FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix | Whole blood | Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. | tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded | GSM7982882 | GSM7982882: Unwounded Larval Zebrafish 4 dpf Danio rerio; RNA Seq | GSM7982882 r1 | GSM7982882 | 1 | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP479046 | loader:fastq load.py | WT-4dpf_S1_L002_R2_001.fastq.gz WT-4dpf_S1_L002_R1_001.fastq.gz | fastq fastq | 12832453413.0 | 109679089.0 | GSM7982882 r2 | 0:28 1:89 | A:3620789787;C:2810897812;G:2929508681;T:3469577031;N:1680102 | 28 | 89 | 3620789787 | 2810897812 | 2929508681 | 3469577031 | 1680102 | SRX22969959 | SRS19936060 | SRA1772557 | University of Wisconsin-Madison | University of Wisconsin-Madison | 2 | 0.0052 | 0.92355 | 0.00192 | 0.16775 | 0.99263 | 0.8253 | 0.37089 | 0.55115 | 28 | 89 | T | B | sc-like readlen | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United States | 2023-12-19 | Multi-stage | Multi-stage | Blood | Hematopoietic System | |||||||||
| 29185 | 29185 | SRR27292314 | SRX22969958 | SRS19936059 | SRP479046 | PRJNA1054617 | Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish | GSE250610 | Transcriptome Analysis | Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de… | pubmed:38922186 | Unwounded Larval Zebrafish 3 dpf | GSM7982881 | source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing | Unwounded Larval Zebrafish 3 dpf | FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix | Whole blood | Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. | tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded | GSM7982881 | GSM7982881: Unwounded Larval Zebrafish 3 dpf Danio rerio; RNA Seq | GSM7982881 r1 | GSM7982881 | 1 | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP479046 | loader:fastq load.py | WT-3dpf_S4_L001_R1_001.fastq.gz WT-3dpf_S4_L001_R2_001.fastq.gz | fastq fastq | 7586138430.0 | 64838790.0 | GSM7982881 r1 | 0:28 1:89 | A:2101749534;C:1692875352;G:1784872358;T:2005308370;N:1332816 | 28 | 89 | 2101749534 | 1692875352 | 1784872358 | 2005308370 | 1332816 | SRX22969958 | SRS19936059 | SRA1772557 | University of Wisconsin-Madison | University of Wisconsin-Madison | 2 | 0.00976 | 0.92096 | 0.00368 | 0.18077 | 0.99356 | 0.83875 | 0.3661 | 0.59073 | 28 | 89 | T | B | sc-like readlen | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United States | 2023-12-19 | Multi-stage | Multi-stage | Blood | Hematopoietic System | |||||||||
| 29186 | 29186 | SRR27292315 | SRX22969958 | SRS19936059 | SRP479046 | PRJNA1054617 | Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish | GSE250610 | Transcriptome Analysis | Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de… | pubmed:38922186 | Unwounded Larval Zebrafish 3 dpf | GSM7982881 | source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing | Unwounded Larval Zebrafish 3 dpf | FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix | Whole blood | Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. | tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded | GSM7982881 | GSM7982881: Unwounded Larval Zebrafish 3 dpf Danio rerio; RNA Seq | GSM7982881 r1 | GSM7982881 | 1 | Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP479046 | loader:fastq load.py | WT-3dpf_S4_L002_R1_001.fastq.gz WT-3dpf_S4_L002_R2_001.fastq.gz | fastq fastq | 7258692168.0 | 62040104.0 | GSM7982881 r2 | 0:28 1:89 | A:2013529524;C:1617959197;G:1704796898;T:1922004726;N:401823 | 28 | 89 | 2013529524 | 1617959197 | 1704796898 | 1922004726 | 401823 | SRX22969958 | SRS19936059 | SRA1772557 | University of Wisconsin-Madison | University of Wisconsin-Madison | 2 | 0.00949 | 0.92207 | 0.00359 | 0.18081 | 0.99375 | 0.83751 | 0.37347 | 0.55889 | 28 | 89 | T | B | sc-like readlen | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United States | 2023-12-19 | Multi-stage | Multi-stage | Blood | Hematopoietic System | |||||||||
| 29820 | 29820 | SRR27499202 | SRX23170207 | SRS20119604 | SRP483288 | PRJNA1063685 | Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment | GSE253039 | Transcriptome Analysis | The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500 generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a slc17a6a while non synchronized neurons showed significantly higher expression of gad1b suggesting that synchronized neurons are primarily glutamatergic while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging and neurons were collected separately with glass pipette. RNA Seq libraries N=10 f… | pubmed:38519480 | non syn 19 1 | GSM8012748 | source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS|geo loc name:missing|collection date:missing | non syn 19 1 | RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample. | brain | TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. | Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. | TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used. | tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS | GSM8012748 | GSM8012748: non syn 19 1; Danio rerio; RNA Seq | GSM8012748 r1 | GSM8012748 | 1 | Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 2000 | SRP483288 | non-syn-19-1_extract_R1.fastq non-syn-19-1_extract_R2.fastq | fastq fastq | 3117719100.0 | 10392397.0 | GSM8012748 r1 | 0:150 1:150 | A:895917474;C:489293250;G:641228744;T:1091230120;N:49512 | 150 | 150 | 895917474 | 489293250 | 641228744 | 1091230120 | 49512 | SRX23170207 | SRS20119604 | SRA1784161 | Neuroscience, School of Medcine, Tongji University, 42508444-9 | Neuroscience, School of Medcine, Tongji University, 42508444-9 | T | B | mate1 technical by mapping diff | illumina | nextseq_v2 | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | China | 2024-01-11 | Multi-stage | Multi-stage | Brain | Nervous System | |||||||||||||||||||||
| 29821 | 29821 | SRR27499203 | SRX23170206 | SRS20119603 | SRP483288 | PRJNA1063685 | Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment | GSE253039 | Transcriptome Analysis | The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500 generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a slc17a6a while non synchronized neurons showed significantly higher expression of gad1b suggesting that synchronized neurons are primarily glutamatergic while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging and neurons were collected separately with glass pipette. RNA Seq libraries N=10 f… | pubmed:38519480 | non syn 10 1 | GSM8012747 | source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS|geo loc name:missing|collection date:missing | non syn 10 1 | RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample. | brain | TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. | Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. | TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used. | tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS | GSM8012747 | GSM8012747: non syn 10 1; Danio rerio; RNA Seq | GSM8012747 r1 | GSM8012747 | 1 | Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 2000 | SRP483288 | non-syn-10-1_S16_L003_R1_001.fastq.gz non-syn-10-1_S16_L003_R2_001.fastq.gz | fastq fastq | 4498404600.0 | 14994682.0 | GSM8012747 r1 | 0:150 1:150 | A:1317989544;C:684597236;G:860222705;T:1635432063;N:163052 | 150 | 150 | 1317989544 | 684597236 | 860222705 | 1635432063 | 163052 | SRX23170206 | SRS20119603 | SRA1784161 | Neuroscience, School of Medcine, Tongji University, 42508444-9 | Neuroscience, School of Medcine, Tongji University, 42508444-9 | T | B | mate1 technical by mapping diff | illumina | nextseq_v2 | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | China | 2024-01-11 | Multi-stage | Multi-stage | Brain | Nervous System | |||||||||||||||||||||
| 29822 | 29822 | SRR27499204 | SRX23170205 | SRS20119602 | SRP483288 | PRJNA1063685 | Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment | GSE253039 | Transcriptome Analysis | The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500 generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a slc17a6a while non synchronized neurons showed significantly higher expression of gad1b suggesting that synchronized neurons are primarily glutamatergic while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging and neurons were collected separately with glass pipette. RNA Seq libraries N=10 f… | pubmed:38519480 | non syn 22 | GSM8012746 | source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS|geo loc name:missing|collection date:missing | non syn 22 | RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample. | brain | TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. | Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. | TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used. | tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS | GSM8012746 | GSM8012746: non syn 22; Danio rerio; RNA Seq | GSM8012746 r1 | GSM8012746 | 1 | Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 2000 | SRP483288 | non-syn-22_S1_L001_R1_001.fastq.gz non-syn-22_S1_L001_R2_001.fastq.gz | fastq fastq | 2450883300.0 | 8169611.0 | GSM8012746 r1 | 0:150 1:150 | A:717072489;C:371259220;G:487966761;T:874532663;N:52167 | 150 | 150 | 717072489 | 371259220 | 487966761 | 874532663 | 52167 | SRX23170205 | SRS20119602 | SRA1784161 | Neuroscience, School of Medcine, Tongji University, 42508444-9 | Neuroscience, School of Medcine, Tongji University, 42508444-9 | T | B | mate1 technical by mapping diff | illumina | nextseq_v2 | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | China | 2024-01-11 | Multi-stage | Multi-stage | Brain | Nervous System | |||||||||||||||||||||
| 29823 | 29823 | SRR27499205 | SRX23170204 | SRS20119601 | SRP483288 | PRJNA1063685 | Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment | GSE253039 | Transcriptome Analysis | The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500 generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a slc17a6a while non synchronized neurons showed significantly higher expression of gad1b suggesting that synchronized neurons are primarily glutamatergic while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging and neurons were collected separately with glass pipette. RNA Seq libraries N=10 f… | pubmed:38519480 | non syn 18 | GSM8012745 | source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS|geo loc name:missing|collection date:missing | non syn 18 | RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample. | brain | TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. | Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. | TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used. | tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS | GSM8012745 | GSM8012745: non syn 18; Danio rerio; RNA Seq | GSM8012745 r1 | GSM8012745 | 1 | Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 2000 | SRP483288 | non-syn-18_S1_L001_R1_001.fastq.gz non-syn-18_S1_L001_R2_001.fastq.gz | fastq fastq | 2481275400.0 | 8270918.0 | GSM8012745 r1 | 0:150 1:150 | A:707890019;C:383065085;G:518277437;T:872001065;N:41794 | 150 | 150 | 707890019 | 383065085 | 518277437 | 872001065 | 41794 | SRX23170204 | SRS20119601 | SRA1784161 | Neuroscience, School of Medcine, Tongji University, 42508444-9 | Neuroscience, School of Medcine, Tongji University, 42508444-9 | T | B | mate1 technical by mapping diff | illumina | nextseq_v2 | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | China | 2024-01-11 | Multi-stage | Multi-stage | Brain | Nervous System | |||||||||||||||||||||
| 29824 | 29824 | SRR27499206 | SRX23170203 | SRS20119600 | SRP483288 | PRJNA1063685 | Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment | GSE253039 | Transcriptome Analysis | The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500 generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a slc17a6a while non synchronized neurons showed significantly higher expression of gad1b suggesting that synchronized neurons are primarily glutamatergic while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging and neurons were collected separately with glass pipette. RNA Seq libraries N=10 f… | pubmed:38519480 | non syn 17 | GSM8012744 | source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS|geo loc name:missing|collection date:missing | non syn 17 | RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample. | brain | TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. | Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. | TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used. | tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS | GSM8012744 | GSM8012744: non syn 17; Danio rerio; RNA Seq | GSM8012744 r1 | GSM8012744 | 1 | Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 2000 | SRP483288 | non-syn-17_S1_L001_R1_001.fastq.gz non-syn-17_S1_L001_R2_001.fastq.gz | fastq fastq | 1902575700.0 | 6341919.0 | GSM8012744 r1 | 0:150 1:150 | A:523356732;C:311424242;G:413587608;T:654191534;N:15584 | 150 | 150 | 523356732 | 311424242 | 413587608 | 654191534 | 15584 | SRX23170203 | SRS20119600 | SRA1784161 | Neuroscience, School of Medcine, Tongji University, 42508444-9 | Neuroscience, School of Medcine, Tongji University, 42508444-9 | T | B | mate1 technical by mapping diff | illumina | nextseq_v2 | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | China | 2024-01-11 | Multi-stage | Multi-stage | Brain | Nervous System | |||||||||||||||||||||
| 29825 | 29825 | SRR27499207 | SRX23170202 | SRS20119599 | SRP483288 | PRJNA1063685 | Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment | GSE253039 | Transcriptome Analysis | The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500 generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a slc17a6a while non synchronized neurons showed significantly higher expression of gad1b suggesting that synchronized neurons are primarily glutamatergic while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging and neurons were collected separately with glass pipette. RNA Seq libraries N=10 f… | pubmed:38519480 | non syn 15 | GSM8012743 | source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS|geo loc name:missing|collection date:missing | non syn 15 | RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample. | brain | TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. | Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. | TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used. | tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS | GSM8012743 | GSM8012743: non syn 15; Danio rerio; RNA Seq | GSM8012743 r1 | GSM8012743 | 1 | Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 2000 | SRP483288 | non-syn-15_S1_L001_R1_001.fastq.gz non-syn-15_S1_L001_R2_001.fastq.gz | fastq fastq | 2644568100.0 | 8815227.0 | GSM8012743 r1 | 0:150 1:150 | A:764042895;C:415507565;G:493804628;T:971168170;N:44842 | 150 | 150 | 764042895 | 415507565 | 493804628 | 971168170 | 44842 | SRX23170202 | SRS20119599 | SRA1784161 | Neuroscience, School of Medcine, Tongji University, 42508444-9 | Neuroscience, School of Medcine, Tongji University, 42508444-9 | T | B | mate1 technical by mapping diff | illumina | nextseq_v2 | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | China | 2024-01-11 | Multi-stage | Multi-stage | Brain | Nervous System | |||||||||||||||||||||
| 29826 | 29826 | SRR27499208 | SRX23170201 | SRS20119598 | SRP483288 | PRJNA1063685 | Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment | GSE253039 | Transcriptome Analysis | The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500 generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a slc17a6a while non synchronized neurons showed significantly higher expression of gad1b suggesting that synchronized neurons are primarily glutamatergic while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging and neurons were collected separately with glass pipette. RNA Seq libraries N=10 f… | pubmed:38519480 | non syn 13 | GSM8012742 | source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS|geo loc name:missing|collection date:missing | non syn 13 | RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample. | brain | TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. | Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. | TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used. | tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS | GSM8012742 | GSM8012742: non syn 13; Danio rerio; RNA Seq | GSM8012742 r1 | GSM8012742 | 1 | Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 2000 | SRP483288 | non-syn-13_S1_L001_R1_001.fastq.gz non-syn-13_S1_L001_R2_001.fastq.gz | fastq fastq | 3344411400.0 | 11148038.0 | GSM8012742 r1 | 0:150 1:150 | A:981997806;C:535742678;G:672084090;T:1154576135;N:10691 | 150 | 150 | 981997806 | 535742678 | 672084090 | 1154576135 | 10691 | SRX23170201 | SRS20119598 | SRA1784161 | Neuroscience, School of Medcine, Tongji University, 42508444-9 | Neuroscience, School of Medcine, Tongji University, 42508444-9 | T | B | mate1 technical by mapping diff | illumina | nextseq_v2 | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | China | 2024-01-11 | Multi-stage | Multi-stage | Brain | Nervous System | |||||||||||||||||||||
| 29827 | 29827 | SRR27499209 | SRX23170200 | SRS20119597 | SRP483288 | PRJNA1063685 | Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment | GSE253039 | Transcriptome Analysis | The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500 generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a slc17a6a while non synchronized neurons showed significantly higher expression of gad1b suggesting that synchronized neurons are primarily glutamatergic while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging and neurons were collected separately with glass pipette. RNA Seq libraries N=10 f… | pubmed:38519480 | non syn 10 | GSM8012741 | source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS|geo loc name:missing|collection date:missing | non syn 10 | RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample. | brain | TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. | Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. | TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used. | tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS | GSM8012741 | GSM8012741: non syn 10; Danio rerio; RNA Seq | GSM8012741 r1 | GSM8012741 | 1 | Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 2000 | SRP483288 | non-syn-10_S17_L003_R1_001.fastq.gz non-syn-10_S17_L003_R2_001.fastq.gz | fastq fastq | 4980891600.0 | 16602972.0 | GSM8012741 r1 | 0:150 1:150 | A:1442162587;C:766015788;G:971257296;T:1801275462;N:180467 | 150 | 150 | 1442162587 | 766015788 | 971257296 | 1801275462 | 180467 | SRX23170200 | SRS20119597 | SRA1784161 | Neuroscience, School of Medcine, Tongji University, 42508444-9 | Neuroscience, School of Medcine, Tongji University, 42508444-9 | T | B | mate1 technical by mapping diff | illumina | nextseq_v2 | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | China | 2024-01-11 | Multi-stage | Multi-stage | Brain | Nervous System |
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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");;