{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Embryo\" and tissue_curation = \"Multi-tissue\"", "rows": [[175, "DRR084197", "DRX078028", "DRS086522", "DRP004758", "PRJDB5490", "Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004758", "Other", "Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.", null, null, "natural paring early sample", "zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate2]", "SAMD00073604", null, "sample name:M 4th|replicate:biological replicate 2", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00073604", "DRX078028", "zebrafish ovary isolated from adult fish natural paring oocyte maturation. 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Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.", null, null, "natural paring early sample", "zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate1]", "SAMD00073598", null, "sample name:M|replicate:biological replicate 1", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00073598", "DRX078022", "zebrafish ovary isolated from adult fish natural paring oocyte maturation. 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A 10 base indexing sequence TCGAAGTGAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC9 WT F sc 1951842|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 13129 8#9", "10325318", "Illumina sequencing of library 10325318  constructed from sample accession ERS460539 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13129 8.  This submission includes reads tagged with the sequence TCGAAGTG.", "qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP003932", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16", "13129_8#9.cram", "cram", 2109545984.0, 16480828.0, "SC RUN 13129 8#9", "0:53 1:75", "A:539694535;C:346663352;G:388843341;T:829045236;N:5299520", 53, 75, null, null, 539694535, 346663352, 388843341, 829045236, 5299520, "ERX557514", "ERS460539", "ERA358077", "SC", "Wellcome Sanger Institute", 2, 0.39712, 0.80906, 0.2298, 0.0288, 0.97575, 0.82292, 0.20258, 0.50014, 53, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2014-09-16", "Zygote", "Embryo", "Multi-tissue", "Multi-system"], [10189, "ERR600684", "ERX557513", "ERS460538", "ERP003932", "PRJEB4632", "Zebrafish oocyte maturation", "Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777", "Transcriptome Analysis", "The data within this study has been generated to study zebrafish oocyte maturation.", null, null, null, null, "SAMEA2537629", "SC", "ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:41:18Z|External Id:SAMEA2537629|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:41:18Z|INSDC status:public|Submitter Id:stI oocytes TC8 buc 4 sc 1951841|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TTCCATTGAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC8 buc 4 sc 1951841|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 13129 8#8", "10325317", "Illumina sequencing of library 10325317  constructed from sample accession ERS460538 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13129 8.  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A 10 base indexing sequence TAGTCTTGAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC7 buc 3 sc 1951840|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 13129 8#7", "10325316", "Illumina sequencing of library 10325316  constructed from sample accession ERS460537 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13129 8.  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A 10 base indexing sequence TGTGGTTGAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC6 buc 2 sc 1951839|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 13129 8#6", "10325315", "Illumina sequencing of library 10325315  constructed from sample accession ERS460536 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13129 8.  This submission includes reads tagged with the sequence TGTGGTTG.", "qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP003932", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16", "13129_8#6.cram", "cram", 2044001792.0, 15968764.0, "SC RUN 13129 8#6", "0:53 1:75", "A:525134102;C:334554692;G:372135205;T:806953076;N:5224717", 53, 75, null, null, 525134102, 334554692, 372135205, 806953076, 5224717, "ERX557511", "ERS460536", "ERA358077", "SC", "Wellcome Sanger Institute", 2, 0.32466, 0.83888, 0.17696, 0.03057, 0.97451, 0.82938, 0.2392, 0.48605, 53, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2014-09-16", "Zygote", "Embryo", "Multi-tissue", "Multi-system"], [10192, "ERR600681", "ERX557510", "ERS460535", "ERP003932", "PRJEB4632", "Zebrafish oocyte maturation", "Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777", "Transcriptome Analysis", "The data within this study has been generated to study zebrafish oocyte maturation.", null, null, null, null, "SAMEA2537626", "SC", "ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:41:18Z|External Id:SAMEA2537626|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:41:18Z|INSDC status:public|Submitter Id:stI oocytes TC5 buc 1 sc 1951838|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. 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This submission includes reads tagged with the sequence TCCTCAAT.", "qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP003932", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16", "13129_8#5.cram", "cram", 2936817024.0, 22943883.0, "SC RUN 13129 8#5", "0:53 1:75", "A:708314449;C:473731341;G:531306146;T:1215982569;N:7482519", 53, 75, null, null, 708314449, 473731341, 531306146, 1215982569, 7482519, "ERX557510", "ERS460535", "ERA358077", "SC", "Wellcome Sanger Institute", 2, 0.38759, 0.88578, 0.22255, 0.03034, 0.9707, 0.80984, 0.2075, 0.47267, 53, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2014-09-16", "Zygote", "Embryo", "Multi-tissue", "Multi-system"], [10193, "ERR600680", "ERX557509", "ERS460534", "ERP003932", "PRJEB4632", "Zebrafish oocyte maturation", "Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777", "Transcriptome Analysis", "The data within this study has been generated to study zebrafish oocyte maturation.", null, null, null, null, "SAMEA2537625", "SC", "ArrayExpress Genotype:Tgbuc:del80|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:57:23Z|External Id:SAMEA2537625|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:57:23Z|INSDC status:public|Submitter Id:stI oocytes TC4 Tg 1 sc 1951837|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. 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This submission includes reads tagged with the sequence TACAGGAT.", "qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP003932", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16", "13129_8#4.cram", "cram", 2384869248.0, 18631791.0, "SC RUN 13129 8#4", "0:53 1:75", "A:579389373;C:378753292;G:429075103;T:991563565;N:6087915", 53, 75, null, null, 579389373, 378753292, 429075103, 991563565, 6087915, "ERX557509", "ERS460534", "ERA358077", "SC", "Wellcome Sanger Institute", 2, 0.48038, 0.84929, 0.28951, 0.03671, 0.97788, 0.81249, 0.13153, 0.4899, 53, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2014-09-16", "Zygote", "Embryo", "Multi-tissue", "Multi-system"], [10194, "ERR600679", "ERX557508", "ERS460533", "ERP003932", "PRJEB4632", "Zebrafish oocyte maturation", "Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777", "Transcriptome Analysis", "The data within this study has been generated to study zebrafish oocyte maturation.", null, null, null, null, "SAMEA2537624", "SC", "ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:42:28Z|External Id:SAMEA2537624|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:42:28Z|INSDC status:public|Submitter Id:stI oocytes TC3 WT 3 sc 1951836|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TAGTGACTAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC3 WT 3 sc 1951836|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 13129 8#3", "10325312", "Illumina sequencing of library 10325312  constructed from sample accession ERS460533 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13129 8.  This submission includes reads tagged with the sequence TAGTGACT.", "qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP003932", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16", "13129_8#3.cram", "cram", 2105031424.0, 16445558.0, "SC RUN 13129 8#3", "0:53 1:75", "A:508334707;C:332423893;G:374815782;T:884154321;N:5302721", 53, 75, null, null, 508334707, 332423893, 374815782, 884154321, 5302721, "ERX557508", "ERS460533", "ERA358077", "SC", "Wellcome Sanger Institute", 2, 0.50684, 0.84751, 0.30664, 0.04222, 0.97853, 0.81343, 0.11336, 0.49639, 53, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2014-09-16", "Zygote", "Embryo", "Multi-tissue", "Multi-system"], [10195, "ERR600678", "ERX557507", "ERS460532", "ERP003932", "PRJEB4632", "Zebrafish oocyte maturation", "Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777", "Transcriptome Analysis", "The data within this study has been generated to study zebrafish oocyte maturation.", null, null, null, null, "SAMEA2537623", "SC", "ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:41:18Z|External Id:SAMEA2537623|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:41:18Z|INSDC status:public|Submitter Id:stI oocytes TC2 WT 2 sc 1951835|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TTCCTGCTAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC2 WT 2 sc 1951835|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 13129 8#2", "10325311", "Illumina sequencing of library 10325311  constructed from sample accession ERS460532 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13129 8.  This submission includes reads tagged with the sequence TTCCTGCT.", "qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP003932", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16", "13129_8#2.cram", "cram", 1616469504.0, 12628668.0, "SC RUN 13129 8#2", "0:53 1:75", "A:415492342;C:254209235;G:288719848;T:653979238;N:4068841", 53, 75, null, null, 415492342, 254209235, 288719848, 653979238, 4068841, "ERX557507", "ERS460532", "ERA358077", "SC", "Wellcome Sanger Institute", 2, 0.44661, 0.81908, 0.25181, 0.0449, 0.96469, 0.80306, 0.22578, 0.49499, 53, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2014-09-16", "Zygote", "Embryo", "Multi-tissue", "Multi-system"], [10196, "ERR600677", "ERX557506", "ERS460531", "ERP003932", "PRJEB4632", "Zebrafish oocyte maturation", "Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777", "Transcriptome Analysis", "The data within this study has been generated to study zebrafish oocyte maturation.", null, null, null, null, "SAMEA2537622", "SC", "ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:57:22Z|External Id:SAMEA2537622|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:57:22Z|INSDC status:public|Submitter Id:stI oocytes TC1 WT 1 sc 1951834|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TGCGATCTAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC1 WT 1 sc 1951834|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 13129 8#1", "10325310", "Illumina sequencing of library 10325310  constructed from sample accession ERS460531 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13129 8.  This submission includes reads tagged with the sequence TGCGATCT.", "qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP003932", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16", "13129_8#1.cram", "cram", 1741512832.0, 13605569.0, "SC RUN 13129 8#1", "0:53 1:75", "A:460247357;C:265029516;G:295203994;T:716636989;N:4394976", 53, 75, null, null, 460247357, 265029516, 295203994, 716636989, 4394976, "ERX557506", "ERS460531", "ERA358077", "SC", "Wellcome Sanger Institute", 2, 0.36591, 0.79177, 0.21838, 0.03785, 0.97569, 0.81095, 0.16098, 0.49496, 53, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2014-09-16", "Zygote", "Embryo", "Multi-tissue", "Multi-system"], [10197, "ERR596433", "ERX553396", "ERS462797", "ERP003932", "PRJEB4632", "Zebrafish oocyte maturation", "Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777", "Transcriptome Analysis", "The data within this study has been generated to study zebrafish oocyte maturation.", null, null, null, null, "SAMEA2547987", "SC", "ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:41:51Z|External Id:SAMEA2547987|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:41:51Z|INSDC status:public|Submitter Id:stI oocytes Fraction9 WT F sc 1971686|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction9 WT F sc 1971686|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "SC EXP 13147 1#9", "10347698", "Illumina sequencing of library 10347698  constructed from sample accession ERS462797 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13147 1.  This submission includes reads tagged with the sequence GATCAG.", "RNA seq dUTP", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP003932", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16", "13147_1#9.cram", "cram", 552103200.0, 1840344.0, "SC RUN 13147 1#9", "0:150 1:150", "A:124691243;C:154385942;G:155440122;T:117585893;N:0", 150, 150, null, null, 124691243, 154385942, 155440122, 117585893, 0, "ERX553396", "ERS462797", "ERA356861", "SC", "Wellcome Sanger Institute", 2, 0.97349, 0.97184, 0.25562, 0.26367, 0.73754, 0.76534, 0.68526, 0.65497, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2014-09-09", "Zygote", "Embryo", "Multi-tissue", "Multi-system"], [10198, "ERR596432", "ERX553395", "ERS462796", "ERP003932", "PRJEB4632", "Zebrafish oocyte maturation", "Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777", "Transcriptome Analysis", "The data within this study has been generated to study zebrafish oocyte maturation.", null, null, null, null, "SAMEA2547986", "SC", "ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:58:35Z|External Id:SAMEA2547986|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:58:35Z|INSDC status:public|Submitter Id:stI oocytes Fraction8 buc 4 sc 1971685|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction8 buc 4 sc 1971685|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "SC EXP 13147 1#8", "10347697", "Illumina sequencing of library 10347697  constructed from sample accession ERS462796 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13147 1.  This submission includes reads tagged with the sequence ACTTGA.", "RNA seq dUTP", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP003932", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16", "13147_1#8.cram", "cram", 625194300.0, 2083981.0, "SC RUN 13147 1#8", "0:150 1:150", "A:145587865;C:170554648;G:171453968;T:137597813;N:6", 150, 150, null, null, 145587865, 170554648, 171453968, 137597813, 6, "ERX553395", "ERS462796", "ERA356861", "SC", "Wellcome Sanger Institute", 2, 0.97066, 0.96788, 0.23219, 0.23823, 0.7205, 0.75623, 0.61734, 0.60233, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2014-09-09", "Zygote", "Embryo", "Multi-tissue", "Multi-system"], [10199, "ERR596431", "ERX553394", "ERS462795", "ERP003932", "PRJEB4632", "Zebrafish oocyte maturation", "Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777", "Transcriptome Analysis", "The data within this study has been generated to study zebrafish oocyte maturation.", null, null, null, null, "SAMEA2547985", "SC", "ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:42:18Z|External Id:SAMEA2547985|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:42:18Z|INSDC status:public|Submitter Id:stI oocytes Fraction7 buc 3 sc 1971684|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction7 buc 3 sc 1971684|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "SC EXP 13147 1#7", "10347696", "Illumina sequencing of library 10347696  constructed from sample accession ERS462795 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13147 1.  This submission includes reads tagged with the sequence CAGATC.", "RNA seq dUTP", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP003932", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16", "13147_1#7.cram", "cram", 498083400.0, 1660278.0, "SC RUN 13147 1#7", "0:150 1:150", "A:127449944;C:127409242;G:133869886;T:109354327;N:1", 150, 150, null, null, 127449944, 127409242, 133869886, 109354327, 1, "ERX553394", "ERS462795", "ERA356861", "SC", "Wellcome Sanger Institute", 2, 0.94952, 0.95502, 0.14913, 0.14846, 0.73807, 0.74572, 0.54621, 0.54335, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2014-09-09", "Zygote", "Embryo", "Multi-tissue", "Multi-system"], [10200, "ERR596430", "ERX553393", "ERS462794", "ERP003932", "PRJEB4632", "Zebrafish oocyte maturation", "Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777", "Transcriptome Analysis", "The data within this study has been generated to study zebrafish oocyte maturation.", null, null, null, null, "SAMEA2547984", "SC", "ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:41:51Z|External Id:SAMEA2547984|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:41:51Z|INSDC status:public|Submitter Id:stI oocytes Fraction6 buc 2 sc 1971683|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction6 buc 2 sc 1971683|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "SC EXP 13147 1#6", "10347695", "Illumina sequencing of library 10347695  constructed from sample accession ERS462794 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13147 1.  This submission includes reads tagged with the sequence GCCAAT.", "RNA seq dUTP", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP003932", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16", "13147_1#6.cram", "cram", 433626600.0, 1445422.0, "SC RUN 13147 1#6", "0:150 1:150", "A:113030099;C:110060861;G:116695113;T:93840526;N:1", 150, 150, null, null, 113030099, 110060861, 116695113, 93840526, 1, "ERX553393", "ERS462794", "ERA356861", "SC", "Wellcome Sanger Institute", 2, 0.94512, 0.95418, 0.13754, 0.13509, 0.76274, 0.77542, 0.54752, 0.54127, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2014-09-09", "Zygote", "Embryo", "Multi-tissue", "Multi-system"], [10201, "ERR596429", "ERX553392", "ERS462793", "ERP003932", "PRJEB4632", "Zebrafish oocyte maturation", "Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777", "Transcriptome Analysis", "The data within this study has been generated to study zebrafish oocyte maturation.", null, null, null, null, "SAMEA2547983", "SC", "ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:58:34Z|External Id:SAMEA2547983|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:58:34Z|INSDC status:public|Submitter Id:stI oocytes Fraction5 buc 1 sc 1971682|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction5 buc 1 sc 1971682|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "SC EXP 13147 1#5", "10347694", "Illumina sequencing of library 10347694  constructed from sample accession ERS462793 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13147 1.  This submission includes reads tagged with the sequence ACAGTG.", "RNA seq dUTP", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP003932", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16", "13147_1#5.cram", "cram", 670533600.0, 2235112.0, "SC RUN 13147 1#5", "0:150 1:150", "A:152057213;C:184952145;G:191337018;T:142187224;N:0", 150, 150, null, null, 152057213, 184952145, 191337018, 142187224, 0, "ERX553392", "ERS462793", "ERA356861", "SC", "Wellcome Sanger Institute", 2, 0.95987, 0.95954, 0.20495, 0.20606, 0.73726, 0.7529, 0.61328, 0.61986, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2014-09-09", "Zygote", "Embryo", "Multi-tissue", "Multi-system"], [10202, "ERR596428", "ERX553391", "ERS462792", "ERP003932", "PRJEB4632", "Zebrafish oocyte maturation", "Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777", "Transcriptome Analysis", "The data within this study has been generated to study zebrafish oocyte maturation.", null, null, null, null, "SAMEA2547982", "SC", "ArrayExpress Genotype:Tgbuc:del80|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:42:18Z|External Id:SAMEA2547982|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:42:18Z|INSDC status:public|Submitter Id:stI oocytes Fraction4 Tg 1 sc 1971681|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction4 Tg 1 sc 1971681|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "SC EXP 13147 1#4", "10347693", "Illumina sequencing of library 10347693  constructed from sample accession ERS462792 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13147 1.  This submission includes reads tagged with the sequence TGACCA.", "RNA seq dUTP", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP003932", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16", "13147_1#4.cram", "cram", 524202300.0, 1747341.0, "SC RUN 13147 1#4", "0:150 1:150", "A:117529161;C:147865152;G:153007969;T:105800018;N:0", 150, 150, null, null, 117529161, 147865152, 153007969, 105800018, 0, "ERX553391", "ERS462792", "ERA356861", "SC", "Wellcome Sanger Institute", 2, 0.95955, 0.96175, 0.21001, 0.20834, 0.76445, 0.78281, 0.70435, 0.68975, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2014-09-09", "Zygote", "Embryo", "Multi-tissue", "Multi-system"], [10203, "ERR596427", "ERX553390", "ERS462791", "ERP003932", "PRJEB4632", "Zebrafish oocyte maturation", "Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777", "Transcriptome Analysis", "The data within this study has been generated to study zebrafish oocyte maturation.", null, null, null, null, "SAMEA2547981", "SC", "ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:41:51Z|External Id:SAMEA2547981|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:41:51Z|INSDC status:public|Submitter Id:stI oocytes Fraction3 WT 3 sc 1971680|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction3 WT 3 sc 1971680|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "SC EXP 13147 1#3", "10347692", "Illumina sequencing of library 10347692  constructed from sample accession ERS462791 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13147 1.  This submission includes reads tagged with the sequence TTAGGC.", "RNA seq dUTP", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP003932", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16", "13147_1#3.cram", "cram", 1142124300.0, 3807081.0, "SC RUN 13147 1#3", "0:150 1:150", "A:239327535;C:334933829;G:339423780;T:228439155;N:1", 150, 150, null, null, 239327535, 334933829, 339423780, 228439155, 1, "ERX553390", "ERS462791", "ERA356861", "SC", "Wellcome Sanger Institute", 2, 0.98041, 0.98099, 0.28225, 0.28585, 0.80273, 0.81012, 0.81256, 0.81436, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2014-09-09", "Zygote", "Embryo", "Multi-tissue", "Multi-system"], [10204, "ERR596426", "ERX553389", "ERS462790", "ERP003932", "PRJEB4632", "Zebrafish oocyte maturation", "Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777", "Transcriptome Analysis", "The data within this study has been generated to study zebrafish oocyte maturation.", null, null, null, null, "SAMEA2547980", "SC", "ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:58:34Z|External Id:SAMEA2547980|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:58:34Z|INSDC status:public|Submitter Id:stI oocytes Fraction2 WT 2 sc 1971679|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction2 WT 2 sc 1971679|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "SC EXP 13147 1#2", "10347691", "Illumina sequencing of library 10347691  constructed from sample accession ERS462790 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13147 1.  This submission includes reads tagged with the sequence CGATGT.", "RNA seq dUTP", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP003932", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16", "13147_1#2.cram", "cram", 714969600.0, 2383232.0, "SC RUN 13147 1#2", "0:150 1:150", "A:151578902;C:207835645;G:217545196;T:138009856;N:1", 150, 150, null, null, 151578902, 207835645, 217545196, 138009856, 1, "ERX553389", "ERS462790", "ERA356861", "SC", "Wellcome Sanger Institute", 2, 0.97925, 0.981, 0.2548, 0.25496, 0.77447, 0.78462, 0.77035, 0.76498, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2014-09-09", "Zygote", "Embryo", "Multi-tissue", "Multi-system"], [10205, "ERR596425", "ERX553388", "ERS462789", "ERP003932", "PRJEB4632", "Zebrafish oocyte maturation", "Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777", "Transcriptome Analysis", "The data within this study has been generated to study zebrafish oocyte maturation.", null, null, null, null, "SAMEA2547979", "SC", "ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:42:18Z|External Id:SAMEA2547979|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:42:18Z|INSDC status:public|Submitter Id:stI oocytes Fraction1 WT 1 sc 1971678|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction1 WT 1 sc 1971678|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "SC EXP 13147 1#1", "10347690", "Illumina sequencing of library 10347690  constructed from sample accession ERS462789 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13147 1.  This submission includes reads tagged with the sequence ATCACG.", "RNA seq dUTP", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP003932", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16", "13147_1#1.cram", "cram", 567682800.0, 1892276.0, "SC RUN 13147 1#1", "0:150 1:150", "A:133087363;C:153887726;G:158264603;T:122443107;N:1", 150, 150, null, null, 133087363, 153887726, 158264603, 122443107, 1, "ERX553388", "ERS462789", "ERA356861", "SC", "Wellcome Sanger Institute", 2, 0.94832, 0.94927, 0.19305, 0.19445, 0.72421, 0.73551, 0.59172, 0.60783, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2014-09-09", "Zygote", "Embryo", "Multi-tissue", "Multi-system"], [25091, "SRR25567703", "SRX21296461", "SRS18545739", "SRP453968", "PRJNA1003386", "Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish", "GSE240329", "Transcriptome Analysis", "To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.", null, "pubmed:38742432", null, "EC  tie1 Homo  replicate 2  RNAseq", "GSM7696246", null, "source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing", "EC  tie1 Homo  replicate 2  RNAseq", "RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.", "homozygous tie1 mutant embryos", null, "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer\u2019s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed", "GSM7696246", "GSM7696246: EC  tie1 Homo  replicate 2  RNAseq; Danio rerio; RNA Seq", "GSM7696246 r1", "GSM7696246", "1", "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP453968", null, null, "413-Tie1-KO2_S4_L001_R1_001.fastq.gz", "fastq", 445428400.0, 5860900.0, "GSM7696246 r1", "0:76", "A:143568074;C:79903177;G:79677344;T:142230186;N:49619", 76, null, null, null, 143568074, 79903177, 79677344, 142230186, 49619, "SRX21296461", "SRS18545739", "SRA1688627", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", 1, 0.75644, null, 0.67481, null, 0.78062, null, 0.49002, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "Japan", "2023-08-08", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [25092, "SRR25567704", "SRX21296461", "SRS18545739", "SRP453968", "PRJNA1003386", "Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish", "GSE240329", "Transcriptome Analysis", "To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.", null, "pubmed:38742432", null, "EC  tie1 Homo  replicate 2  RNAseq", "GSM7696246", null, "source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing", "EC  tie1 Homo  replicate 2  RNAseq", "RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.", "homozygous tie1 mutant embryos", null, "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer\u2019s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed", "GSM7696246", "GSM7696246: EC  tie1 Homo  replicate 2  RNAseq; Danio rerio; RNA Seq", "GSM7696246 r1", "GSM7696246", "1", "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP453968", null, null, "413-Tie1-KO2_S4_L002_R1_001.fastq.gz", "fastq", 436280280.0, 5740530.0, "GSM7696246 r2", "0:76", "A:140668025;C:78248456;G:77919880;T:139381210;N:62709", 76, null, null, null, 140668025, 78248456, 77919880, 139381210, 62709, "SRX21296461", "SRS18545739", "SRA1688627", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", 1, 0.75737, null, 0.67543, null, 0.77796, null, 0.494, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "Japan", "2023-08-08", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [25093, "SRR25567705", "SRX21296461", "SRS18545739", "SRP453968", "PRJNA1003386", "Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish", "GSE240329", "Transcriptome Analysis", "To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.", null, "pubmed:38742432", null, "EC  tie1 Homo  replicate 2  RNAseq", "GSM7696246", null, "source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing", "EC  tie1 Homo  replicate 2  RNAseq", "RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.", "homozygous tie1 mutant embryos", null, "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer\u2019s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed", "GSM7696246", "GSM7696246: EC  tie1 Homo  replicate 2  RNAseq; Danio rerio; RNA Seq", "GSM7696246 r1", "GSM7696246", "1", "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP453968", null, null, "413-Tie1-KO2_S4_L003_R1_001.fastq.gz", "fastq", 453115800.0, 5962050.0, "GSM7696246 r3", "0:76", "A:145977328;C:81331359;G:81042932;T:144726596;N:37585", 76, null, null, null, 145977328, 81331359, 81042932, 144726596, 37585, "SRX21296461", "SRS18545739", "SRA1688627", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", 1, 0.75941, null, 0.67812, null, 0.78255, null, 0.49198, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "Japan", "2023-08-08", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [25094, "SRR25567706", "SRX21296461", "SRS18545739", "SRP453968", "PRJNA1003386", "Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish", "GSE240329", "Transcriptome Analysis", "To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.", null, "pubmed:38742432", null, "EC  tie1 Homo  replicate 2  RNAseq", "GSM7696246", null, "source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing", "EC  tie1 Homo  replicate 2  RNAseq", "RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.", "homozygous tie1 mutant embryos", null, "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer\u2019s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed", "GSM7696246", "GSM7696246: EC  tie1 Homo  replicate 2  RNAseq; Danio rerio; RNA Seq", "GSM7696246 r1", "GSM7696246", "1", "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP453968", null, null, "413-Tie1-KO2_S4_L004_R1_001.fastq.gz", "fastq", 451629316.0, 5942491.0, "GSM7696246 r4", "0:76", "A:145539227;C:81081378;G:80692220;T:144283694;N:32797", 76, null, null, null, 145539227, 81081378, 80692220, 144283694, 32797, "SRX21296461", "SRS18545739", "SRA1688627", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", 1, 0.75907, null, 0.67763, null, 0.78074, null, 0.49757, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "Japan", "2023-08-08", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [25095, "SRR25567707", "SRX21296460", "SRS18545738", "SRP453968", "PRJNA1003386", "Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish", "GSE240329", "Transcriptome Analysis", "To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.", null, "pubmed:38742432", null, "EC  tie1 Homo  replicate 1  RNAseq", "GSM7696245", null, "source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing", "EC  tie1 Homo  replicate 1  RNAseq", "RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.", "homozygous tie1 mutant embryos", null, "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer\u2019s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed", "GSM7696245", "GSM7696245: EC  tie1 Homo  replicate 1  RNAseq; Danio rerio; RNA Seq", "GSM7696245 r1", "GSM7696245", "1", "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP453968", null, null, "412-Tie1-KO1_S3_L001_R1_001.fastq.gz", "fastq", 438903344.0, 5775044.0, "GSM7696245 r1", "0:76", "A:141636851;C:79318996;G:78779375;T:139120411;N:47711", 76, null, null, null, 141636851, 79318996, 78779375, 139120411, 47711, "SRX21296460", "SRS18545738", "SRA1688627", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", 1, 0.76357, null, 0.65866, null, 0.76238, null, 0.48958, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "Japan", "2023-08-08", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [25096, "SRR25567708", "SRX21296460", "SRS18545738", "SRP453968", "PRJNA1003386", "Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish", "GSE240329", "Transcriptome Analysis", "To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.", null, "pubmed:38742432", null, "EC  tie1 Homo  replicate 1  RNAseq", "GSM7696245", null, "source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing", "EC  tie1 Homo  replicate 1  RNAseq", "RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.", "homozygous tie1 mutant embryos", null, "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer\u2019s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed", "GSM7696245", "GSM7696245: EC  tie1 Homo  replicate 1  RNAseq; Danio rerio; RNA Seq", "GSM7696245 r1", "GSM7696245", "1", "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP453968", null, null, "412-Tie1-KO1_S3_L002_R1_001.fastq.gz", "fastq", 429344216.0, 5649266.0, "GSM7696245 r2", "0:76", "A:138620131;C:77579442;G:76950101;T:136131396;N:63146", 76, null, null, null, 138620131, 77579442, 76950101, 136131396, 63146, "SRX21296460", "SRS18545738", "SRA1688627", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", 1, 0.76216, null, 0.65728, null, 0.76132, null, 0.4958, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "Japan", "2023-08-08", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [25097, "SRR25567709", "SRX21296460", "SRS18545738", "SRP453968", "PRJNA1003386", "Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish", "GSE240329", "Transcriptome Analysis", "To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.", null, "pubmed:38742432", null, "EC  tie1 Homo  replicate 1  RNAseq", "GSM7696245", null, "source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing", "EC  tie1 Homo  replicate 1  RNAseq", "RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.", "homozygous tie1 mutant embryos", null, "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer\u2019s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed", "GSM7696245", "GSM7696245: EC  tie1 Homo  replicate 1  RNAseq; Danio rerio; RNA Seq", "GSM7696245 r1", "GSM7696245", "1", "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP453968", null, null, "412-Tie1-KO1_S3_L003_R1_001.fastq.gz", "fastq", 446301792.0, 5872392.0, "GSM7696245 r3", "0:76", "A:143941333;C:80689335;G:80111561;T:141523625;N:35938", 76, null, null, null, 143941333, 80689335, 80111561, 141523625, 35938, "SRX21296460", "SRS18545738", "SRA1688627", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", 1, 0.76416, null, 0.65858, null, 0.76177, null, 0.48634, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "Japan", "2023-08-08", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [25098, "SRR25567710", "SRX21296460", "SRS18545738", "SRP453968", "PRJNA1003386", "Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish", "GSE240329", "Transcriptome Analysis", "To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.", null, "pubmed:38742432", null, "EC  tie1 Homo  replicate 1  RNAseq", "GSM7696245", null, "source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing", "EC  tie1 Homo  replicate 1  RNAseq", "RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.", "homozygous tie1 mutant embryos", null, "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer\u2019s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed", "GSM7696245", "GSM7696245: EC  tie1 Homo  replicate 1  RNAseq; Danio rerio; RNA Seq", "GSM7696245 r1", "GSM7696245", "1", "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP453968", null, null, "412-Tie1-KO1_S3_L004_R1_001.fastq.gz", "fastq", 443971252.0, 5841727.0, "GSM7696245 r4", "0:76", "A:143197029;C:80287228;G:79639533;T:140816381;N:31081", 76, null, null, null, 143197029, 80287228, 79639533, 140816381, 31081, "SRX21296460", "SRS18545738", "SRA1688627", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", 1, 0.77093, null, 0.66467, null, 0.76081, null, 0.49407, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "Japan", "2023-08-08", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [25099, "SRR25567711", "SRX21296459", "SRS18545737", "SRP453968", "PRJNA1003386", "Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish", "GSE240329", "Transcriptome Analysis", "To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.", null, "pubmed:38742432", null, "EC  tie1 WT/Het  replicate 2  RNAseq", "GSM7696244", null, "source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing", "EC  tie1 WT/Het  replicate 2  RNAseq", "RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.", "wild type and heterozygous siblings", null, "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer\u2019s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed", "GSM7696244", "GSM7696244: EC  tie1 WT/Het  replicate 2  RNAseq; Danio rerio; RNA Seq", "GSM7696244 r1", "GSM7696244", "1", "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP453968", null, null, "411-Tie1-WT-HT2_S2_L001_R1_001.fastq.gz", "fastq", 392537796.0, 5164971.0, "GSM7696244 r1", "0:76", "A:124144181;C:72762157;G:72562894;T:123025322;N:43242", 76, null, null, null, 124144181, 72762157, 72562894, 123025322, 43242, "SRX21296459", "SRS18545737", "SRA1688627", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", 1, 0.78106, null, 0.59772, null, 0.73553, null, 0.48949, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "Japan", "2023-08-08", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [25100, "SRR25567712", "SRX21296459", "SRS18545737", "SRP453968", "PRJNA1003386", "Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish", "GSE240329", "Transcriptome Analysis", "To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.", null, "pubmed:38742432", null, "EC  tie1 WT/Het  replicate 2  RNAseq", "GSM7696244", null, "source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing", "EC  tie1 WT/Het  replicate 2  RNAseq", "RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.", "wild type and heterozygous siblings", null, "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer\u2019s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed", "GSM7696244", "GSM7696244: EC  tie1 WT/Het  replicate 2  RNAseq; Danio rerio; RNA Seq", "GSM7696244 r1", "GSM7696244", "1", "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP453968", null, null, "411-Tie1-WT-HT2_S2_L002_R1_001.fastq.gz", "fastq", 384487572.0, 5059047.0, "GSM7696244 r2", "0:76", "A:121620414;C:71266999;G:70967086;T:120577709;N:55364", 76, null, null, null, 121620414, 71266999, 70967086, 120577709, 55364, "SRX21296459", "SRS18545737", "SRA1688627", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", 1, 0.77986, null, 0.59517, null, 0.73547, null, 0.48651, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "Japan", "2023-08-08", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [25101, "SRR25567713", "SRX21296459", "SRS18545737", "SRP453968", "PRJNA1003386", "Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish", "GSE240329", "Transcriptome Analysis", "To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.", null, "pubmed:38742432", null, "EC  tie1 WT/Het  replicate 2  RNAseq", "GSM7696244", null, "source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing", "EC  tie1 WT/Het  replicate 2  RNAseq", "RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.", "wild type and heterozygous siblings", null, "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer\u2019s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed", "GSM7696244", "GSM7696244: EC  tie1 WT/Het  replicate 2  RNAseq; Danio rerio; RNA Seq", "GSM7696244 r1", "GSM7696244", "1", "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP453968", null, null, "411-Tie1-WT-HT2_S2_L003_R1_001.fastq.gz", "fastq", 399939360.0, 5262360.0, "GSM7696244 r3", "0:76", "A:126400057;C:74196301;G:73931308;T:125379595;N:32099", 76, null, null, null, 126400057, 74196301, 73931308, 125379595, 32099, "SRX21296459", "SRS18545737", "SRA1688627", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", 1, 0.77917, null, 0.59465, null, 0.7359, null, 0.48952, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "Japan", "2023-08-08", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [25102, "SRR25567714", "SRX21296459", "SRS18545737", "SRP453968", "PRJNA1003386", "Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish", "GSE240329", "Transcriptome Analysis", "To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.", null, "pubmed:38742432", null, "EC  tie1 WT/Het  replicate 2  RNAseq", "GSM7696244", null, "source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing", "EC  tie1 WT/Het  replicate 2  RNAseq", "RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.", "wild type and heterozygous siblings", null, "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer\u2019s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed", "GSM7696244", "GSM7696244: EC  tie1 WT/Het  replicate 2  RNAseq; Danio rerio; RNA Seq", "GSM7696244 r1", "GSM7696244", "1", "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP453968", null, null, "411-Tie1-WT-HT2_S2_L004_R1_001.fastq.gz", "fastq", 398035712.0, 5237312.0, "GSM7696244 r4", "0:76", "A:125843687;C:73845902;G:73489490;T:124828195;N:28438", 76, null, null, null, 125843687, 73845902, 73489490, 124828195, 28438, "SRX21296459", "SRS18545737", "SRA1688627", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", 1, 0.77934, null, 0.59613, null, 0.73608, null, 0.48475, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "Japan", "2023-08-08", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [25103, "SRR25567715", "SRX21296458", "SRS18545736", "SRP453968", "PRJNA1003386", "Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish", "GSE240329", "Transcriptome Analysis", "To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.", null, "pubmed:38742432", null, "EC  tie1 WT/Het  replicate 1  RNAseq", "GSM7696243", null, "source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing", "EC  tie1 WT/Het  replicate 1  RNAseq", "RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.", "wild type and heterozygous siblings", null, "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer\u2019s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed", "GSM7696243", "GSM7696243: EC  tie1 WT/Het  replicate 1  RNAseq; Danio rerio; RNA Seq", "GSM7696243 r1", "GSM7696243", "1", "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP453968", null, null, "410-Tie1-WT-HT1_S1_L001_R1_001.fastq.gz", "fastq", 412291944.0, 5424894.0, "GSM7696243 r1", "0:76", "A:129182868;C:77123147;G:77053023;T:128887593;N:45313", 76, null, null, null, 129182868, 77123147, 77053023, 128887593, 45313, "SRX21296458", "SRS18545736", "SRA1688627", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", 1, 0.79085, null, 0.52962, null, 0.7349, null, 0.48594, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "Japan", "2023-08-08", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [25104, "SRR25567716", "SRX21296458", "SRS18545736", "SRP453968", "PRJNA1003386", "Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish", "GSE240329", "Transcriptome Analysis", "To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.", null, "pubmed:38742432", null, "EC  tie1 WT/Het  replicate 1  RNAseq", "GSM7696243", null, "source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing", "EC  tie1 WT/Het  replicate 1  RNAseq", "RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.", "wild type and heterozygous siblings", null, "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer\u2019s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed", "GSM7696243", "GSM7696243: EC  tie1 WT/Het  replicate 1  RNAseq; Danio rerio; RNA Seq", "GSM7696243 r1", "GSM7696243", "1", "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP453968", null, null, "410-Tie1-WT-HT1_S1_L002_R1_001.fastq.gz", "fastq", 404294768.0, 5319668.0, "GSM7696243 r2", "0:76", "A:126685179;C:75658897;G:75455501;T:126437486;N:57705", 76, null, null, null, 126685179, 75658897, 75455501, 126437486, 57705, "SRX21296458", "SRS18545736", "SRA1688627", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", 1, 0.79163, null, 0.52938, null, 0.73304, null, 0.48118, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "Japan", "2023-08-08", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [25105, "SRR25567717", "SRX21296458", "SRS18545736", "SRP453968", "PRJNA1003386", "Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish", "GSE240329", "Transcriptome Analysis", "To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.", null, "pubmed:38742432", null, "EC  tie1 WT/Het  replicate 1  RNAseq", "GSM7696243", null, "source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing", "EC  tie1 WT/Het  replicate 1  RNAseq", "RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.", "wild type and heterozygous siblings", null, "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer\u2019s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed", "GSM7696243", "GSM7696243: EC  tie1 WT/Het  replicate 1  RNAseq; Danio rerio; RNA Seq", "GSM7696243 r1", "GSM7696243", "1", "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP453968", null, null, "410-Tie1-WT-HT1_S1_L003_R1_001.fastq.gz", "fastq", 419693128.0, 5522278.0, "GSM7696243 r3", "0:76", "A:131491219;C:78551884;G:78434940;T:131179828;N:35257", 76, null, null, null, 131491219, 78551884, 78434940, 131179828, 35257, "SRX21296458", "SRS18545736", "SRA1688627", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", 1, 0.79077, null, 0.52836, null, 0.73419, null, 0.48215, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "Japan", "2023-08-08", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [25106, "SRR25567718", "SRX21296458", "SRS18545736", "SRP453968", "PRJNA1003386", "Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish", "GSE240329", "Transcriptome Analysis", "To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.", null, "pubmed:38742432", null, "EC  tie1 WT/Het  replicate 1  RNAseq", "GSM7696243", null, "source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing", "EC  tie1 WT/Het  replicate 1  RNAseq", "RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.", "wild type and heterozygous siblings", null, "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer\u2019s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed", "GSM7696243", "GSM7696243: EC  tie1 WT/Het  replicate 1  RNAseq; Danio rerio; RNA Seq", "GSM7696243 r1", "GSM7696243", "1", "Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP453968", null, null, "410-Tie1-WT-HT1_S1_L004_R1_001.fastq.gz", "fastq", 418155268.0, 5502043.0, "GSM7696243 r4", "0:76", "A:130978746;C:78285682;G:78062725;T:130798846;N:29269", 76, null, null, null, 130978746, 78285682, 78062725, 130798846, 29269, "SRX21296458", "SRS18545736", "SRA1688627", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", "Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute", 1, 0.78728, null, 0.52541, null, 0.73484, null, 0.48813, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "Japan", "2023-08-08", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [29808, "SRR27450807", "SRX23122487", "SRS20076037", "SRP482328", "PRJNA1061565", "Akt is the main kinase mediating the embryonic specification of artery cells", "GSE252648", "Transcriptome Analysis", "This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.", null, "pubmed:39101673", null, "Zebrafish  EC  24hpf  Aktmutant", "GSM8004755", null, "source name:FAC sorted cells|tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:Aktmutant|geo loc name:missing|collection date:missing", "Zebrafish  EC  24hpf  Aktmutant", "The barcoded processing  gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes  features and matrix", "FAC sorted cells", "No treatments", "Wild type  aktmutant  Tgkdrl:mCherry tissue  were dissected at 24 hpf. Dissected  tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3\u2019 Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3\u2019 Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell  10x genomics", "Normal zebrafish growth condition", "tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:Aktmutant", "GSM8004755", "GSM8004755: Zebrafish  EC  24hpf  Aktmutant; Danio rerio; RNA Seq", "GSM8004755 r1", "GSM8004755", "1", "Wild type  aktmutant  Tgkdrl:mCherry tissue  were dissected at 24 hpf. Dissected  tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell  10x genomics", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP482328", null, "loader:fastq load.py", "mu1-23-19_DRT_S2_L001_I1_001.fastq.gz mu1-23-19_DRT_S2_L001_R1_001.fastq.gz mu1-23-19_DRT_S2_L001_R2_001.fastq.gz", "fastq fastq fastq", 23281472741.0, 183318683.0, "GSM8004755 r1", "0:8 1:28 2:91", "A:4703583066;C:3702175361;G:3998796644;T:4271932211;N:5512871", 8, 28, 91, null, 4703583066, 3702175361, 3998796644, 4271932211, 5512871, "SRX23122487", "SRS20076037", "SRA1780571", "Nicoli lab, School of Medicine, Yale University", "Nicoli lab, School of Medicine, Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-05", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [29809, "SRR27450808", "SRX23122487", "SRS20076037", "SRP482328", "PRJNA1061565", "Akt is the main kinase mediating the embryonic specification of artery cells", "GSE252648", "Transcriptome Analysis", "This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.", null, "pubmed:39101673", null, "Zebrafish  EC  24hpf  Aktmutant", "GSM8004755", null, "source name:FAC sorted cells|tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:Aktmutant|geo loc name:missing|collection date:missing", "Zebrafish  EC  24hpf  Aktmutant", "The barcoded processing  gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes  features and matrix", "FAC sorted cells", "No treatments", "Wild type  aktmutant  Tgkdrl:mCherry tissue  were dissected at 24 hpf. Dissected  tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3\u2019 Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3\u2019 Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell  10x genomics", "Normal zebrafish growth condition", "tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:Aktmutant", "GSM8004755", "GSM8004755: Zebrafish  EC  24hpf  Aktmutant; Danio rerio; RNA Seq", "GSM8004755 r1", "GSM8004755", "1", "Wild type  aktmutant  Tgkdrl:mCherry tissue  were dissected at 24 hpf. Dissected  tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell  10x genomics", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP482328", null, "loader:fastq load.py", "mu1-23-19_DRT_S2_L002_I1_001.fastq.gz mu1-23-19_DRT_S2_L002_R1_001.fastq.gz mu1-23-19_DRT_S2_L002_R2_001.fastq.gz", "fastq fastq fastq", 21009317138.0, 165427694.0, "GSM8004755 r2", "0:8 1:28 2:91", "A:4231955850;C:3363548064;G:3603913589;T:3849411287;N:5091364", 8, 28, 91, null, 4231955850, 3363548064, 3603913589, 3849411287, 5091364, "SRX23122487", "SRS20076037", "SRA1780571", "Nicoli lab, School of Medicine, Yale University", "Nicoli lab, School of Medicine, Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-05", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [29810, "SRR27450809", "SRX23122486", "SRS20076036", "SRP482328", "PRJNA1061565", "Akt is the main kinase mediating the embryonic specification of artery cells", "GSE252648", "Transcriptome Analysis", "This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.", null, "pubmed:39101673", null, "Zebrafish  EC  24hpf  WT", "GSM8004754", null, "source name:FAC sorted cells|tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:WT|geo loc name:missing|collection date:missing", "Zebrafish  EC  24hpf  WT", "The barcoded processing  gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes  features and matrix", "FAC sorted cells", "No treatments", "Wild type  aktmutant  Tgkdrl:mCherry tissue  were dissected at 24 hpf. Dissected  tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3\u2019 Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3\u2019 Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell  10x genomics", "Normal zebrafish growth condition", "tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:WT", "GSM8004754", "GSM8004754: Zebrafish  EC  24hpf  WT; Danio rerio; RNA Seq", "GSM8004754 r1", "GSM8004754", "1", "Wild type  aktmutant  Tgkdrl:mCherry tissue  were dissected at 24 hpf. Dissected  tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell  10x genomics", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP482328", null, "loader:fastq load.py", "wt1-23-19_DRT_S1_L001_I1_001.fastq.gz wt1-23-19_DRT_S1_L001_R1_001.fastq.gz wt1-23-19_DRT_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 22261273232.0, 175285616.0, "GSM8004754 r1", "0:8 1:28 2:91", "A:4475749188;C:3578353646;G:3836029871;T:4055646794;N:5211557", 8, 28, 91, null, 4475749188, 3578353646, 3836029871, 4055646794, 5211557, "SRX23122486", "SRS20076036", "SRA1780571", "Nicoli lab, School of Medicine, Yale University", "Nicoli lab, School of Medicine, Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-05", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [29811, "SRR27450810", "SRX23122486", "SRS20076036", "SRP482328", "PRJNA1061565", "Akt is the main kinase mediating the embryonic specification of artery cells", "GSE252648", "Transcriptome Analysis", "This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.", null, "pubmed:39101673", null, "Zebrafish  EC  24hpf  WT", "GSM8004754", null, "source name:FAC sorted cells|tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:WT|geo loc name:missing|collection date:missing", "Zebrafish  EC  24hpf  WT", "The barcoded processing  gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes  features and matrix", "FAC sorted cells", "No treatments", "Wild type  aktmutant  Tgkdrl:mCherry tissue  were dissected at 24 hpf. Dissected  tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3\u2019 Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3\u2019 Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell  10x genomics", "Normal zebrafish growth condition", "tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:WT", "GSM8004754", "GSM8004754: Zebrafish  EC  24hpf  WT; Danio rerio; RNA Seq", "GSM8004754 r1", "GSM8004754", "1", "Wild type  aktmutant  Tgkdrl:mCherry tissue  were dissected at 24 hpf. Dissected  tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell  10x genomics", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP482328", null, "loader:fastq load.py", "wt1-23-19_DRT_S1_L002_I1_001.fastq.gz wt1-23-19_DRT_S1_L002_R1_001.fastq.gz wt1-23-19_DRT_S1_L002_R2_001.fastq.gz", "fastq fastq fastq", 20084395188.0, 158144844.0, "GSM8004754 r2", "0:8 1:28 2:91", "A:4028678970;C:3250176957;G:3455600305;T:3651884457;N:4840115", 8, 28, 91, null, 4028678970, 3250176957, 3455600305, 3651884457, 4840115, "SRX23122486", "SRS20076036", "SRA1780571", "Nicoli lab, School of Medicine, Yale University", "Nicoli lab, School of Medicine, Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-05", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [29909, "SRR27592934", "SRX23261746", "SRS20163710", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep11", "GSM8020192", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep11", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types", "GSM8020192", "GSM8020192: deaf1  2 dpf  rep11; Danio rerio; RNA Seq", "GSM8020192 r1", "GSM8020192", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-wt_D28_S56_R1_001.fastq.gz", "fastq", 4475806200.0, 44758062.0, "GSM8020192 r1", "0:100", "A:1106171674;C:1156870042;G:1092472583;T:1120212338;N:79563", 100, null, null, null, 1106171674, 1156870042, 1092472583, 1120212338, 79563, "SRX23261746", "SRS20163710", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29910, "SRR27592935", "SRX23261745", "SRS20163711", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep10", "GSM8020191", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep10", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types", "GSM8020191", "GSM8020191: deaf1  2 dpf  rep10; Danio rerio; RNA Seq", "GSM8020191 r1", "GSM8020191", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-wt_D27_S55_R1_001.fastq.gz", "fastq", 4001586700.0, 40015867.0, "GSM8020191 r1", "0:100", "A:1000059012;C:1020300240;G:981249122;T:999909425;N:68901", 100, null, null, null, 1000059012, 1020300240, 981249122, 999909425, 68901, "SRX23261745", "SRS20163711", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29911, "SRR27592936", "SRX23261744", "SRS20163709", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep9", "GSM8020190", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep9", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types", "GSM8020190", "GSM8020190: deaf1  2 dpf  rep9; Danio rerio; RNA Seq", "GSM8020190 r1", "GSM8020190", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-wt_D26_S54_R1_001.fastq.gz", "fastq", 3716740300.0, 37167403.0, "GSM8020190 r1", "0:100", "A:930732486;C:940157658;G:908687307;T:937097122;N:65727", 100, null, null, null, 930732486, 940157658, 908687307, 937097122, 65727, "SRX23261744", "SRS20163709", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29912, "SRR27592937", "SRX23261743", "SRS20163708", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep8", "GSM8020189", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep8", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous", "GSM8020189", "GSM8020189: deaf1  2 dpf  rep8; Danio rerio; RNA Seq", "GSM8020189 r1", "GSM8020189", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-hom_D25_S53_R1_001.fastq.gz", "fastq", 3741485000.0, 37414850.0, "GSM8020189 r1", "0:100", "A:929440558;C:958986044;G:914039968;T:938952561;N:65869", 100, null, null, null, 929440558, 958986044, 914039968, 938952561, 65869, "SRX23261743", "SRS20163708", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29913, "SRR27592938", "SRX23261742", "SRS20163707", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep7", "GSM8020188", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep7", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous", "GSM8020188", "GSM8020188: deaf1  2 dpf  rep7; Danio rerio; RNA Seq", "GSM8020188 r1", "GSM8020188", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-hom_D24_S52_R1_001.fastq.gz", "fastq", 2971991400.0, 29719914.0, "GSM8020188 r1", "0:100", "A:738636815;C:755836125;G:729168292;T:748297854;N:52314", 100, null, null, null, 738636815, 755836125, 729168292, 748297854, 52314, "SRX23261742", "SRS20163707", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29914, "SRR27592939", "SRX23261741", "SRS20163706", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep6", "GSM8020187", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep6", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous", "GSM8020187", "GSM8020187: deaf1  2 dpf  rep6; Danio rerio; RNA Seq", "GSM8020187 r1", "GSM8020187", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-hom_D23_S51_R1_001.fastq.gz", "fastq", 4134397800.0, 41343978.0, "GSM8020187 r1", "0:100", "A:1032735373;C:1051188374;G:1016197596;T:1034203095;N:73362", 100, null, null, null, 1032735373, 1051188374, 1016197596, 1034203095, 73362, "SRX23261741", "SRS20163706", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29915, "SRR27592940", "SRX23261740", "SRS20163705", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep5", "GSM8020186", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep5", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous", "GSM8020186", "GSM8020186: deaf1  2 dpf  rep5; Danio rerio; RNA Seq", "GSM8020186 r1", "GSM8020186", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-hom_D22_S50_R1_001.fastq.gz", "fastq", 3631624500.0, 36316245.0, "GSM8020186 r1", "0:100", "A:901094303;C:929956244;G:893844528;T:906664233;N:65192", 100, null, null, null, 901094303, 929956244, 893844528, 906664233, 65192, "SRX23261740", "SRS20163705", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29916, "SRR27592941", "SRX23261739", "SRS20163704", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep4", "GSM8020185", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep4", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous", "GSM8020185", "GSM8020185: deaf1  2 dpf  rep4; Danio rerio; RNA Seq", "GSM8020185 r1", "GSM8020185", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-hom_D21_S49_R1_001.fastq.gz", "fastq", 3349609200.0, 33496092.0, "GSM8020185 r1", "0:100", "A:835857971;C:854981364;G:824035698;T:834673793;N:60374", 100, null, null, null, 835857971, 854981364, 824035698, 834673793, 60374, "SRX23261739", "SRS20163704", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29917, "SRR27592942", "SRX23261738", "SRS20163703", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep3", "GSM8020184", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i heterozygous|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep3", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i heterozygous", "GSM8020184", "GSM8020184: deaf1  2 dpf  rep3; Danio rerio; RNA Seq", "GSM8020184 r1", "GSM8020184", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-het_D20_S48_R1_001.fastq.gz", "fastq", 3371713300.0, 33717133.0, "GSM8020184 r1", "0:100", "A:839050016;C:857965663;G:828869795;T:845766740;N:61086", 100, null, null, null, 839050016, 857965663, 828869795, 845766740, 61086, "SRX23261738", "SRS20163703", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29918, "SRR27592943", "SRX23261737", "SRS20163701", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep2", "GSM8020183", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i heterozygous|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep2", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i heterozygous", "GSM8020183", "GSM8020183: deaf1  2 dpf  rep2; Danio rerio; RNA Seq", "GSM8020183 r1", "GSM8020183", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-het_D18_S46_R1_001.fastq.gz", "fastq", 3756501100.0, 37565011.0, "GSM8020183 r1", "0:100", "A:938612608;C:949004833;G:927692516;T:941125085;N:66058", 100, null, null, null, 938612608, 949004833, 927692516, 941125085, 66058, "SRX23261737", "SRS20163701", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29919, "SRR27592944", "SRX23261736", "SRS20163702", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep1", "GSM8020182", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i heterozygous|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep1", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i heterozygous", "GSM8020182", "GSM8020182: deaf1  2 dpf  rep1; Danio rerio; RNA Seq", "GSM8020182 r1", "GSM8020182", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-het_D17_S45_R1_001.fastq.gz", "fastq", 3378074100.0, 33780741.0, "GSM8020182 r1", "0:100", "A:839320911;C:859028175;G:836373251;T:843291522;N:60241", 100, null, null, null, 839320911, 859028175, 836373251, 843291522, 60241, "SRX23261736", "SRS20163702", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29920, "SRR27592945", "SRX23261735", "SRS20163699", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep13", "GSM8020181", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p wild types|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep13", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p wild types", "GSM8020181", "GSM8020181: deaf1 t238p  2 dpf  rep13; Danio rerio; RNA Seq", "GSM8020181 r1", "GSM8020181", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-wt_ST4.fastq.gz", "fastq", 2522881653.0, 33818740.0, "GSM8020181 r1", "0:74.60", "A:655207900;C:616856238;G:613068980;T:637525231;N:223304", 74, null, null, null, 655207900, 616856238, 613068980, 637525231, 223304, "SRX23261735", "SRS20163699", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29921, "SRR27592946", "SRX23261734", "SRS20163698", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep12", "GSM8020180", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p wild types|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep12", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p wild types", "GSM8020180", "GSM8020180: deaf1 t238p  2 dpf  rep12; Danio rerio; RNA Seq", "GSM8020180 r1", "GSM8020180", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-wt_ST3.fastq.gz", "fastq", 3232696302.0, 43332777.0, "GSM8020180 r1", "0:74.60", "A:838706781;C:792017578;G:780975426;T:820709157;N:287360", 74, null, null, null, 838706781, 792017578, 780975426, 820709157, 287360, "SRX23261734", "SRS20163698", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29922, "SRR27592947", "SRX23261733", "SRS20163700", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep11", "GSM8020179", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p wild types|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep11", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p wild types", "GSM8020179", "GSM8020179: deaf1 t238p  2 dpf  rep11; Danio rerio; RNA Seq", "GSM8020179 r1", "GSM8020179", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-wt_ST2.fastq.gz", "fastq", 3105671470.0, 41634840.0, "GSM8020179 r1", "0:74.59", "A:797054679;C:770109006;G:759275000;T:778955169;N:277616", 74, null, null, null, 797054679, 770109006, 759275000, 778955169, 277616, "SRX23261733", "SRS20163700", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29923, "SRR27592948", "SRX23261732", "SRS20163697", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep10", "GSM8020178", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p wild types|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep10", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p wild types", "GSM8020178", "GSM8020178: deaf1 t238p  2 dpf  rep10; Danio rerio; RNA Seq", "GSM8020178 r1", "GSM8020178", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-wt_ST1.fastq.gz", "fastq", 3499217864.0, 46905154.0, "GSM8020178 r1", "0:74.60", "A:893360259;C:869418642;G:860403580;T:875711902;N:323481", 74, null, null, null, 893360259, 869418642, 860403580, 875711902, 323481, "SRX23261732", "SRS20163697", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29924, "SRR27592949", "SRX23261731", "SRS20163696", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep9", "GSM8020177", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p homozygous|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep9", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p homozygous", "GSM8020177", "GSM8020177: deaf1 t238p  2 dpf  rep9; Danio rerio; RNA Seq", "GSM8020177 r1", "GSM8020177", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-hom_ST8.fastq.gz", "fastq", 3268771798.0, 43820118.0, "GSM8020177 r1", "0:74.60", "A:847366551;C:800849702;G:791226044;T:829037606;N:291895", 74, null, null, null, 847366551, 800849702, 791226044, 829037606, 291895, "SRX23261731", "SRS20163696", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29925, "SRR27592950", "SRX23261730", "SRS20163695", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep8", "GSM8020176", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p homozygous|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep8", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p homozygous", "GSM8020176", "GSM8020176: deaf1 t238p  2 dpf  rep8; Danio rerio; RNA Seq", "GSM8020176 r1", "GSM8020176", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-hom_ST7.fastq.gz", "fastq", 2027174325.0, 27178466.0, "GSM8020176 r1", "0:74.59", "A:525317640;C:498055852;G:491357881;T:512263813;N:179139", 74, null, null, null, 525317640, 498055852, 491357881, 512263813, 179139, "SRX23261730", "SRS20163695", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29926, "SRR27592951", "SRX23261729", "SRS20163694", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep7", "GSM8020175", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p homozygous|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep7", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p homozygous", "GSM8020175", "GSM8020175: deaf1 t238p  2 dpf  rep7; Danio rerio; RNA Seq", "GSM8020175 r1", "GSM8020175", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-hom_ST6.fastq.gz", "fastq", 2787340348.0, 37363599.0, "GSM8020175 r1", "0:74.60", "A:722896986;C:681138747;G:674833627;T:708219281;N:251707", 74, null, null, null, 722896986, 681138747, 674833627, 708219281, 251707, "SRX23261729", "SRS20163694", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29927, "SRR27592952", "SRX23261728", "SRS20163693", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep6", "GSM8020174", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p homozygous|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep6", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p homozygous", "GSM8020174", "GSM8020174: deaf1 t238p  2 dpf  rep6; Danio rerio; RNA Seq", "GSM8020174 r1", "GSM8020174", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-hom_ST5.fastq.gz", "fastq", 2977171544.0, 39908640.0, "GSM8020174 r1", "0:74.60", "A:770250088;C:731344480;G:721594408;T:753713587;N:268981", 74, null, null, null, 770250088, 731344480, 721594408, 753713587, 268981, "SRX23261728", "SRS20163693", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29928, "SRR27592953", "SRX23261727", "SRS20163692", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep5", "GSM8020173", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p heterozygous|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep5", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p heterozygous", "GSM8020173", "GSM8020173: deaf1 t238p  2 dpf  rep5; Danio rerio; RNA Seq", "GSM8020173 r1", "GSM8020173", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-het_ST9.fastq.gz", "fastq", 2546529762.0, 34141024.0, "GSM8020173 r1", "0:74.59", "A:665391714;C:618921995;G:614059292;T:647931593;N:225168", 74, null, null, null, 665391714, 618921995, 614059292, 647931593, 225168, "SRX23261727", "SRS20163692", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29929, "SRR27592954", "SRX23261726", "SRS20163691", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep4", "GSM8020172", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p heterozygous|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep4", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p heterozygous", "GSM8020172", "GSM8020172: deaf1 t238p  2 dpf  rep4; Danio rerio; RNA Seq", "GSM8020172 r1", "GSM8020172", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-het_ST13.fastq.gz", "fastq", 3176861738.0, 42588753.0, "GSM8020172 r1", "0:74.59", "A:831927955;C:768758728;G:763547713;T:812339162;N:288180", 74, null, null, null, 831927955, 768758728, 763547713, 812339162, 288180, "SRX23261726", "SRS20163691", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29930, "SRR27592955", "SRX23261725", "SRS20163690", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep3", "GSM8020171", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p heterozygous|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep3", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p heterozygous", "GSM8020171", "GSM8020171: deaf1 t238p  2 dpf  rep3; Danio rerio; RNA Seq", "GSM8020171 r1", "GSM8020171", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-het_ST12.fastq.gz", "fastq", 1136232560.0, 15234548.0, "GSM8020171 r1", "0:74.58", "A:297385645;C:276022399;G:273402666;T:289320311;N:101539", 74, null, null, null, 297385645, 276022399, 273402666, 289320311, 101539, "SRX23261725", "SRS20163690", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29931, "SRR27592956", "SRX23261724", "SRS20163689", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep2", "GSM8020170", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p heterozygous|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep2", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p heterozygous", "GSM8020170", "GSM8020170: deaf1 t238p  2 dpf  rep2; Danio rerio; RNA Seq", "GSM8020170 r1", "GSM8020170", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-het_ST11.fastq.gz", "fastq", 2735749019.0, 36680185.0, "GSM8020170 r1", "0:74.58", "A:721197113;C:659588175;G:652875625;T:701848626;N:239480", 74, null, null, null, 721197113, 659588175, 652875625, 701848626, 239480, "SRX23261724", "SRS20163689", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29932, "SRR27592957", "SRX23261723", "SRS20163688", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep1", "GSM8020169", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p heterozygous|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep1", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p heterozygous", "GSM8020169", "GSM8020169: deaf1 t238p  2 dpf  rep1; Danio rerio; RNA Seq", "GSM8020169 r1", "GSM8020169", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-het_ST10.fastq.gz", "fastq", 3369699901.0, 45178398.0, "GSM8020169 r1", "0:74.59", "A:883991145;C:814741172;G:809532162;T:861133903;N:301519", 74, null, null, null, 883991145, 814741172, 809532162, 861133903, 301519, "SRX23261723", "SRS20163688", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29947, "SRR27592972", "SRX23261708", "SRS20163673", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep13", "GSM8020168", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y wild types|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep13", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y wild types", "GSM8020168", "GSM8020168: deaf1 c207y  2 dpf  rep13; Danio rerio; RNA Seq", "GSM8020168 r1", "GSM8020168", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-wt_B2_S14_R1_001.fastq.gz", "fastq", 2963811367.0, 29344667.0, "GSM8020168 r1", "0:101", "A:803333990;C:685431342;G:677569210;T:797384558;N:92267", 101, null, null, null, 803333990, 685431342, 677569210, 797384558, 92267, "SRX23261708", "SRS20163673", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29948, "SRR27592973", "SRX23261707", "SRS20163672", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep12", "GSM8020167", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y wild types|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep12", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y wild types", "GSM8020167", "GSM8020167: deaf1 c207y  2 dpf  rep12; Danio rerio; RNA Seq", "GSM8020167 r1", "GSM8020167", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-wt_B1_S13_R1_001.fastq.gz", "fastq", 3184165289.0, 31526389.0, "GSM8020167 r1", "0:101", "A:847208990;C:751109498;G:736855605;T:848892893;N:98303", 101, null, null, null, 847208990, 751109498, 736855605, 848892893, 98303, "SRX23261707", "SRS20163672", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29949, "SRR27592974", "SRX23261706", "SRS20163671", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep11", "GSM8020166", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y wild types|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep11", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y wild types", "GSM8020166", "GSM8020166: deaf1 c207y  2 dpf  rep11; Danio rerio; RNA Seq", "GSM8020166 r1", "GSM8020166", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-wt_A12_S12_R1_001.fastq.gz", "fastq", 3115838183.0, 30849883.0, "GSM8020166 r1", "0:101", "A:846133299;C:724401184;G:709966835;T:835240904;N:95961", 101, null, null, null, 846133299, 724401184, 709966835, 835240904, 95961, "SRX23261706", "SRS20163671", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29950, "SRR27592975", "SRX23261705", "SRS20163670", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep10", "GSM8020165", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y wild types|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep10", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y wild types", "GSM8020165", "GSM8020165: deaf1 c207y  2 dpf  rep10; Danio rerio; RNA Seq", "GSM8020165 r1", "GSM8020165", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-wt_A11_S11_R1_001.fastq.gz", "fastq", 2767984184.0, 27405784.0, "GSM8020165 r1", "0:101", "A:753665483;C:638171516;G:626255827;T:749805524;N:85834", 101, null, null, null, 753665483, 638171516, 626255827, 749805524, 85834, "SRX23261705", "SRS20163670", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29951, "SRR27592976", "SRX23261704", "SRS20163669", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep9", "GSM8020164", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y wild types|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep9", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y wild types", "GSM8020164", "GSM8020164: deaf1 c207y  2 dpf  rep9; Danio rerio; RNA Seq", "GSM8020164 r1", "GSM8020164", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-wt_A10_S10_R1_001.fastq.gz", "fastq", 5417478400.0, 53638400.0, "GSM8020164 r1", "0:101", "A:1459560082;C:1269220844;G:1235271759;T:1453256921;N:168794", 101, null, null, null, 1459560082, 1269220844, 1235271759, 1453256921, 168794, "SRX23261704", "SRS20163669", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29952, "SRR27592977", "SRX23261703", "SRS20163668", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep8", "GSM8020163", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y homozygous|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep8", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y homozygous", "GSM8020163", "GSM8020163: deaf1 c207y  2 dpf  rep8; Danio rerio; RNA Seq", "GSM8020163 r1", "GSM8020163", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-hom_A9_S9_R1_001.fastq.gz", "fastq", 2417886167.0, 23939467.0, "GSM8020163 r1", "0:101", "A:657342317;C:558713775;G:547590726;T:654164599;N:74750", 101, null, null, null, 657342317, 558713775, 547590726, 654164599, 74750, "SRX23261703", "SRS20163668", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29953, "SRR27592978", "SRX23261702", "SRS20163667", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep7", "GSM8020162", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y homozygous|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep7", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y homozygous", "GSM8020162", "GSM8020162: deaf1 c207y  2 dpf  rep7; Danio rerio; RNA Seq", "GSM8020162 r1", "GSM8020162", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-hom_A8_S8_R1_001.fastq.gz", "fastq", 3601305288.0, 35656488.0, "GSM8020162 r1", "0:101", "A:974139857;C:839029639;G:822572729;T:965450738;N:112325", 101, null, null, null, 974139857, 839029639, 822572729, 965450738, 112325, "SRX23261702", "SRS20163667", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29954, "SRR27592979", "SRX23261701", "SRS20163666", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep6", "GSM8020161", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y homozygous|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep6", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y homozygous", "GSM8020161", "GSM8020161: deaf1 c207y  2 dpf  rep6; Danio rerio; RNA Seq", "GSM8020161 r1", "GSM8020161", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-hom_A6_S6_R1_001.fastq.gz", "fastq", 2545549965.0, 25203465.0, "GSM8020161 r1", "0:101", "A:689302325;C:596907356;G:578571204;T:680690103;N:78977", 101, null, null, null, 689302325, 596907356, 578571204, 680690103, 78977, "SRX23261701", "SRS20163666", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29955, "SRR27592980", "SRX23261700", "SRS20163665", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep5", "GSM8020160", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y heterozygous|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep5", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y heterozygous", "GSM8020160", "GSM8020160: deaf1 c207y  2 dpf  rep5; Danio rerio; RNA Seq", "GSM8020160 r1", "GSM8020160", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-het_A5_S5_R1_001.fastq.gz", "fastq", 3102857158.0, 30721358.0, "GSM8020160 r1", "0:101", "A:850838897;C:712670459;G:688515516;T:850736210;N:96076", 101, null, null, null, 850838897, 712670459, 688515516, 850736210, 96076, "SRX23261700", "SRS20163665", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29956, "SRR27592981", "SRX23261699", "SRS20163664", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep4", "GSM8020159", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y heterozygous|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep4", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y heterozygous", "GSM8020159", "GSM8020159: deaf1 c207y  2 dpf  rep4; Danio rerio; RNA Seq", "GSM8020159 r1", "GSM8020159", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-het_A4_S4_R1_001.fastq.gz", "fastq", 3415651633.0, 33818333.0, "GSM8020159 r1", "0:101", "A:933225760;C:786732356;G:770845968;T:924742081;N:105468", 101, null, null, null, 933225760, 786732356, 770845968, 924742081, 105468, "SRX23261699", "SRS20163664", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29957, "SRR27592982", "SRX23261698", "SRS20163663", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep3", "GSM8020158", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y heterozygous|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep3", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y heterozygous", "GSM8020158", "GSM8020158: deaf1 c207y  2 dpf  rep3; Danio rerio; RNA Seq", "GSM8020158 r1", "GSM8020158", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-het_A3_S3_R1_001.fastq.gz", "fastq", 3429734972.0, 33957772.0, "GSM8020158 r1", "0:101", "A:920850547;C:802940416;G:790735026;T:915103526;N:105457", 101, null, null, null, 920850547, 802940416, 790735026, 915103526, 105457, "SRX23261698", "SRS20163663", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29958, "SRR27592983", "SRX23261697", "SRS20163662", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep2", "GSM8020157", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y heterozygous|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep2", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y heterozygous", "GSM8020157", "GSM8020157: deaf1 c207y  2 dpf  rep2; Danio rerio; RNA Seq", "GSM8020157 r1", "GSM8020157", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-het_A2_S2_R1_001.fastq.gz", "fastq", 2810870602.0, 27830402.0, "GSM8020157 r1", "0:101", "A:742011214;C:673773327;G:656344142;T:738655690;N:86229", 101, null, null, null, 742011214, 673773327, 656344142, 738655690, 86229, "SRX23261697", "SRS20163662", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29959, "SRR27592984", "SRX23261696", "SRS20163661", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep1", "GSM8020156", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y heterozygous|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep1", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y heterozygous", "GSM8020156", "GSM8020156: deaf1 c207y  2 dpf  rep1; Danio rerio; RNA Seq", "GSM8020156 r1", "GSM8020156", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-het_A1_S1_R1_001.fastq.gz", "fastq", 4234517819.0, 41925919.0, "GSM8020156 r1", "0:101", "A:1104853000;C:1023572758;G:1001000314;T:1104961067;N:130680", 101, null, null, null, 1104853000, 1023572758, 1001000314, 1104961067, 130680, "SRX23261696", "SRS20163661", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29993, "SRR27593018", "SRX23261662", "SRS20163627", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep13", "GSM8020194", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep13", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types", "GSM8020194", "GSM8020194: deaf1  2 dpf  rep13; Danio rerio; RNA Seq", "GSM8020194 r1", "GSM8020194", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-wt_D30_S58_R1_001.fastq.gz", "fastq", 4417470800.0, 44174708.0, "GSM8020194 r1", "0:100", "A:1088757969;C:1142271720;G:1089301455;T:1097060536;N:79120", 100, null, null, null, 1088757969, 1142271720, 1089301455, 1097060536, 79120, "SRX23261662", "SRS20163627", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29994, "SRR27593019", "SRX23261661", "SRS20163626", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep12", "GSM8020193", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep12", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types", "GSM8020193", "GSM8020193: deaf1  2 dpf  rep12; Danio rerio; RNA Seq", "GSM8020193 r1", "GSM8020193", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-wt_D29_S57_R1_001.fastq.gz", "fastq", 4218209500.0, 42182095.0, "GSM8020193 r1", "0:100", "A:1040374012;C:1082175747;G:1042489373;T:1053094232;N:76136", 100, null, null, null, 1040374012, 1082175747, 1042489373, 1053094232, 76136, "SRX23261661", "SRS20163626", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [33700, "SRR30599779", "SRX26022472", "SRS22594191", "SRP531514", "PRJNA1158727", "CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30", "GSE276705", "Transcriptome Analysis", "Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.", null, null, null, "ebf3a wt  2 dpf  rep 2", "GSM8504324", null, "source name:upper body with eyes  15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a wild types|geo loc name:missing|collection date:missing", "ebf3a wt  2 dpf  rep 2", "Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "upper body with eyes  15 20 embryos pooled", null, "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "tissue:upper body with eyes|age:2 dpf|genotype:ebf3a wild types", "GSM8504324", "GSM8504324: ebf3a wt  2 dpf  rep 2; Danio rerio; RNA Seq", "GSM8504324 r1", "GSM8504324", "1", "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP531514", null, null, "Ebf-WT-2-2dpf_R1_001.fastq.gz Ebf-WT-2-2dpf_R2_001.fastq.gz", "fastq fastq", 22635570600.0, 75451902.0, "GSM8504324 r1", "0:150 1:150", "A:6279354286;C:5013138453;G:5250498169;T:6092284847;N:294845", 150, 150, null, null, 6279354286, 5013138453, 5250498169, 6092284847, 294845, "SRX26022472", "SRS22594191", "SRA1966071", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-09-09", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [33701, "SRR30599780", "SRX26022471", "SRS22594190", "SRP531514", "PRJNA1158727", "CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30", "GSE276705", "Transcriptome Analysis", "Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.", null, null, null, "ebf3a wt  2 dpf  rep 1", "GSM8504323", null, "source name:upper body with eyes  15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a wild types|geo loc name:missing|collection date:missing", "ebf3a wt  2 dpf  rep 1", "Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "upper body with eyes  15 20 embryos pooled", null, "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "tissue:upper body with eyes|age:2 dpf|genotype:ebf3a wild types", "GSM8504323", "GSM8504323: ebf3a wt  2 dpf  rep 1; Danio rerio; RNA Seq", "GSM8504323 r1", "GSM8504323", "1", "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP531514", null, null, "Ebf-WT-1-2dpf_R1_001.fastq.gz Ebf-WT-1-2dpf_R2_001.fastq.gz", "fastq fastq", 19711425600.0, 65704752.0, "GSM8504323 r1", "0:150 1:150", "A:5541464229;C:4291380685;G:4497372769;T:5380954703;N:253214", 150, 150, null, null, 5541464229, 4291380685, 4497372769, 5380954703, 253214, "SRX26022471", "SRS22594190", "SRA1966071", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-09-09", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [33702, "SRR30599781", "SRX26022470", "SRS22594189", "SRP531514", "PRJNA1158727", "CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30", "GSE276705", "Transcriptome Analysis", "Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.", null, null, null, "ebf3a het  2 dpf  rep 2", "GSM8504322", null, "source name:upper body with eyes  15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a heterozygous|geo loc name:missing|collection date:missing", "ebf3a het  2 dpf  rep 2", "Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "upper body with eyes  15 20 embryos pooled", null, "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "tissue:upper body with eyes|age:2 dpf|genotype:ebf3a heterozygous", "GSM8504322", "GSM8504322: ebf3a het  2 dpf  rep 2; Danio rerio; RNA Seq", "GSM8504322 r1", "GSM8504322", "1", "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP531514", null, null, "Ebf-HET-2-2dpf_R1_001.fastq.gz Ebf-HET-2-2dpf_R2_001.fastq.gz", "fastq fastq", 15108144300.0, 50360481.0, "GSM8504322 r1", "0:150 1:150", "A:4240605272;C:3297282748;G:3449975456;T:4120084716;N:196108", 150, 150, null, null, 4240605272, 3297282748, 3449975456, 4120084716, 196108, "SRX26022470", "SRS22594189", "SRA1966071", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-09-09", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [33703, "SRR30599782", "SRX26022469", "SRS22594188", "SRP531514", "PRJNA1158727", "CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30", "GSE276705", "Transcriptome Analysis", "Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.", null, null, null, "ebf3a het  2 dpf  rep 1", "GSM8504321", null, "source name:upper body with eyes  15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a heterozygous|geo loc name:missing|collection date:missing", "ebf3a het  2 dpf  rep 1", "Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "upper body with eyes  15 20 embryos pooled", null, "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "tissue:upper body with eyes|age:2 dpf|genotype:ebf3a heterozygous", "GSM8504321", "GSM8504321: ebf3a het  2 dpf  rep 1; Danio rerio; RNA Seq", "GSM8504321 r1", "GSM8504321", "1", "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP531514", null, null, "Ebf-HET-1-2dpf_R1_001.fastq.gz Ebf-HET-1-2dpf_R2_001.fastq.gz", "fastq fastq", 16538340600.0, 55127802.0, "GSM8504321 r1", "0:150 1:150", "A:4633062848;C:3617047326;G:3792365071;T:4495647394;N:217961", 150, 150, null, null, 4633062848, 3617047326, 3792365071, 4495647394, 217961, "SRX26022469", "SRS22594188", "SRA1966071", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-09-09", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [33704, "SRR30599783", "SRX26022468", "SRS22594186", "SRP531514", "PRJNA1158727", "CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30", "GSE276705", "Transcriptome Analysis", "Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.", null, null, null, "ebf3a hom  2 dpf  rep 2", "GSM8504320", null, "source name:upper body with eyes  15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a homozygous|geo loc name:missing|collection date:missing", "ebf3a hom  2 dpf  rep 2", "Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "upper body with eyes  15 20 embryos pooled", null, "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "tissue:upper body with eyes|age:2 dpf|genotype:ebf3a homozygous", "GSM8504320", "GSM8504320: ebf3a hom  2 dpf  rep 2; Danio rerio; RNA Seq", "GSM8504320 r1", "GSM8504320", "1", "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP531514", null, null, "Ebf-HOMO-2-2dpf_R1_001.fastq.gz Ebf-HOMO-2-2dpf_R2_001.fastq.gz", "fastq fastq", 14586421200.0, 48621404.0, "GSM8504320 r1", "0:150 1:150", "A:4099529019;C:3162437766;G:3348146726;T:3976118566;N:189123", 150, 150, null, null, 4099529019, 3162437766, 3348146726, 3976118566, 189123, "SRX26022468", "SRS22594186", "SRA1966071", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-09-09", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [33705, "SRR30599784", "SRX26022467", "SRS22594187", "SRP531514", "PRJNA1158727", "CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30", "GSE276705", "Transcriptome Analysis", "Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.", null, null, null, "ebf3a hom  2 dpf  rep 1", "GSM8504319", null, "source name:upper body with eyes  15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a homozygous|geo loc name:missing|collection date:missing", "ebf3a hom  2 dpf  rep 1", "Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "upper body with eyes  15 20 embryos pooled", null, "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "tissue:upper body with eyes|age:2 dpf|genotype:ebf3a homozygous", "GSM8504319", "GSM8504319: ebf3a hom  2 dpf  rep 1; Danio rerio; RNA Seq", "GSM8504319 r1", "GSM8504319", "1", "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP531514", null, null, "Ebf-HOMO-1-2dpf_R1_001.fastq.gz Ebf-HOMO-1-2dpf_R2_001.fastq.gz", "fastq fastq", 14235405000.0, 47451350.0, "GSM8504319 r1", "0:150 1:150", "A:3937137116;C:3134793115;G:3336004625;T:3827286589;N:183555", 150, 150, null, null, 3937137116, 3134793115, 3336004625, 3827286589, 183555, "SRX26022467", "SRS22594187", "SRA1966071", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-09-09", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [34551, "SRR32104356", "SRX27449954", "SRS23876475", "SRP559533", "PRJNA1214751", "Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq]", "GSE287815", "Transcriptome Analysis", "During vertebrate development  the heart primarily arises from mesoderm  with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives.  Here  by integrating bulk and single cell RNAseq with ATAC seq  we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1  sox9a  tfap2a and ets1. Notably  we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore  expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together  our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination  with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry   were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.", null, null, null, "17hpf Positive CNC 3", "GSM8751787", null, "source name:cardiac neural crest from midbrain hindbrain boundary to somite 6|tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +|geo loc name:missing|collection date:missing", "17hpf Positive CNC 3", "Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples", "cardiac neural crest from midbrain hindbrain boundary to somite 6", null, "mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.", null, "tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +", "GSM8751787", "GSM8751787: 17hpf Positive CNC 3; Danio rerio; RNA Seq", "GSM8751787 r1", "GSM8751787", "1", "mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP559533", null, null, "Sox10_pos_17hpf_CNC_3_22028_combined_filtered.fastq.gz", "fastq", 5836253400.0, 58362534.0, "GSM8751787 r1", "0:100", "A:1666874971;C:1250406201;G:1263794016;T:1655113176;N:65036", 100, null, null, null, 1666874971, 1250406201, 1263794016, 1655113176, 65036, "SRX27449954", "SRS23876475", "SRA2058978", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2025-01-23", "Segmentation", "Embryo", "Multi-tissue", "Multi-system"], [34552, "SRR32104357", "SRX27449953", "SRS23876474", "SRP559533", "PRJNA1214751", "Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq]", "GSE287815", "Transcriptome Analysis", "During vertebrate development  the heart primarily arises from mesoderm  with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives.  Here  by integrating bulk and single cell RNAseq with ATAC seq  we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1  sox9a  tfap2a and ets1. Notably  we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore  expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together  our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination  with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry   were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.", null, null, null, "17hpf Positive CNC 2", "GSM8751786", null, "source name:cardiac neural crest from midbrain hindbrain boundary to somite 6|tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +|geo loc name:missing|collection date:missing", "17hpf Positive CNC 2", "Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples", "cardiac neural crest from midbrain hindbrain boundary to somite 6", null, "mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.", null, "tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +", "GSM8751786", "GSM8751786: 17hpf Positive CNC 2; Danio rerio; RNA Seq", "GSM8751786 r1", "GSM8751786", "1", "mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP559533", null, null, "Sox10_pos_17hpf_CNC_2_21338_combined_filtered.fastq.gz", "fastq", 2444486550.0, 48889731.0, "GSM8751786 r1", "0:50", "A:706384494;C:515182895;G:525593789;T:697319091;N:6281", 50, null, null, null, 706384494, 515182895, 525593789, 697319091, 6281, "SRX27449953", "SRS23876474", "SRA2058978", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2025-01-23", "Segmentation", "Embryo", "Multi-tissue", "Multi-system"], [34553, "SRR32104358", "SRX27449952", "SRS23876472", "SRP559533", "PRJNA1214751", "Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq]", "GSE287815", "Transcriptome Analysis", "During vertebrate development  the heart primarily arises from mesoderm  with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives.  Here  by integrating bulk and single cell RNAseq with ATAC seq  we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1  sox9a  tfap2a and ets1. Notably  we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore  expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together  our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination  with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry   were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.", null, null, null, "17hpf Positive CNC 1", "GSM8751785", null, "source name:cardiac neural crest from midbrain hindbrain boundary to somite 6|tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +|geo loc name:missing|collection date:missing", "17hpf Positive CNC 1", "Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples", "cardiac neural crest from midbrain hindbrain boundary to somite 6", null, "mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.", null, "tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +", "GSM8751785", "GSM8751785: 17hpf Positive CNC 1; Danio rerio; RNA Seq", "GSM8751785 r1", "GSM8751785", "1", "mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP559533", null, null, "Sox10_pos_17hpf_CNC_1_21309_combined_filtered.fastq.gz", "fastq", 3136080950.0, 62721619.0, "GSM8751785 r1", "0:50", "A:867446661;C:707750289;G:716376649;T:844460193;N:47158", 50, null, null, null, 867446661, 707750289, 716376649, 844460193, 47158, "SRX27449952", "SRS23876472", "SRA2058978", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2025-01-23", "Segmentation", "Embryo", "Multi-tissue", "Multi-system"], [46219, "SRR6507314", "SRX3595756", "SRS2864146", "SRP131267", "PRJNA431425", "tp53 deficiency causes a wide tumor spectrum and elevates embryonal rhabdomyosarcoma metastasis in zebrafish", "GSE109581", "Transcriptome Analysis", "We generated tp53 deletion mutant zebrafish that spontaneously develop malignant peripheral nerve sheath tumors  angiosarcomas  germ cell tumors  and an aggressive Natural Killer cell leukemia not previously reported in zebrafish. Each tumor type efficiently engrafted into syngeneic recipient zebrafish and shared gene expression signatures with predicted cells of origin. Overall design: We generated a complete null tp53 deletion allele in syngeneic CG1 strain zebrafish using TALEN endonucleases. The list of tumors spontaneously developed in these tp53del/del animals included malignant peripheral nerve sheath tumors MPNSTs  angiosarcomas  germ cell tumors  and Natural Killer cell leukemia. We obtained 3 MPNSTs samples MPNST 1  MPNST 2 and MPNST 3  2 angiosarcoma samples Angiosarcoma 1 and Angiosarcoma 2  3 leukemia samples Leukemia 1  Leukemia 2 and Leukemia 3  and 1 sample of germ cell tumor GermCell 1. We also assessed the role of tp53 in kRASG12D induced human embryonal rhabdomyosarcoma ERMS using large scale cell transplantation assays and live fluorescent imaging over time. We obtained 3 ERMS samples ERMS 1  ERMS 2 and ERMS 3. All these tumor samples were compared to 3 background CG1 samples samples WholeFish 1  WholeFish 2 and WholeFish 3.", null, "pubmed:30192230", null, "GermCell 1", "GSM2946795", null, "tissue:germ cell tumor|genotype:CG1 tp53 homozygous mutant|tumor type:spontaneous|procedure:primary transplant  GFP FACS sorted", "GermCell 1", "Reads were aligned with STAR v2.4.0; PCR duplicates were removed with Picard v1.95 and reads aligning to ribosomal RNA were removed with RSeQC; gene counts were obtained from reads with an alignment quality of at least 10 using featureCounts and transformed to transcript per million TPM units. Genome build: GRCz10 Supplementary files format and content: Counts matrix provided as supplementary file.", "germ cell tumor", "Tissue was harvested using 90% PBS + 5% FBS. FACS sorting was performed to obtain tumor cell fraction with 85% purity and 90% viability.", "Total RNA was extracted using RLT buffer Qiagen and purified using RNeasy kit Qiagen as per manufacturer instructions Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit", "Animals were raised at 28 degrees celcius", "genotype:CG1 tp53 homozygous mutant|tumor type:spontaneous|procedure:primary transplant  GFP FACS sorted", "GSM2946795", "GSM2946795: GermCell 1; Danio rerio; RNA Seq", "GSM2946795", null, "1", "Total RNA was extracted using RLT buffer Qiagen and purified using RNeasy kit Qiagen as per manufacturer instructions Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit", "GEO Accession:GSM2946795", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131267", null, null, "GermCell_1.bam", "bam", 3209068354.0, 15886477.0, "GSM2946795 r1", "0:101 1:101", "A:840598884;C:754814967;G:771176149;T:842218625;N:259729", 101, 101, null, null, 840598884, 754814967, 771176149, 842218625, 259729, "SRX3595756", "SRS2864146", "SRA652013", "GEO", "Pathology, Massachusetts General Hospital", 2, 0.9446, 0.94929, 0.07879, 0.07672, 0.6518, 0.65287, 0.47991, 0.48302, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-01-24", "Undetermined", "Embryo", "Multi-tissue", "Multi-system"], [49611, "SRR7989641", "SRX4820831", "SRS3895222", "SRP164769", "PRJNA495391", "Wnt/\u00df catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling", "GSE121041", "Transcriptome Analysis", "Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development  but also relevant for vascular and neurodegenerative diseases. However  beyond the early requirement of Wnt signaling for brain capillary development  there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation.  By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling  we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation.   In the absence of Wnt signaling  premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis  whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO", null, "pubmed:30451830;pubmed:38570687", null, "IWR 1 rep3", "GSM3424991", null, "source name:brain endothelial cells|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf", "IWR 1 rep3", "Raw reads were assessed for quality  adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene", "brain endothelial cells", null, "Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank\u2019s Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 \u00b0C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80\u00b0C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.", null, "lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf", "GSM3424991", "GSM3424991: IWR 1 rep3; Danio rerio; RNA Seq", "GSM3424991", null, "1", "Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank's Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 \u00b0C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80\u00b0C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.", "GEO Accession:GSM3424991", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP164769", null, null, "vanHollebeke_IWR_4_R1.fastq.gz", "fastq", 2256000713.0, 30503539.0, "GSM3424991 r1", "0:73.96 1:0", "A:657293471;C:471495202;G:469388740;T:657813037;N:10263", 73, 0, null, null, 657293471, 471495202, 469388740, 657813037, 10263, "SRX4820831", "SRS3895222", "SRA791232", "GEO", "MPI for heart and lung research", 1, 0.82891, null, 0.22262, null, 0.78894, null, 0.52843, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2018-10-09", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [49612, "SRR7989640", "SRX4820830", "SRS3895220", "SRP164769", "PRJNA495391", "Wnt/\u00df catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling", "GSE121041", "Transcriptome Analysis", "Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development  but also relevant for vascular and neurodegenerative diseases. However  beyond the early requirement of Wnt signaling for brain capillary development  there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation.  By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling  we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation.   In the absence of Wnt signaling  premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis  whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO", null, "pubmed:30451830;pubmed:38570687", null, "IWR 1 rep2", "GSM3424990", null, "source name:brain endothelial cells|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf", "IWR 1 rep2", "Raw reads were assessed for quality  adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene", "brain endothelial cells", null, "Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank\u2019s Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 \u00b0C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80\u00b0C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.", null, "lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf", "GSM3424990", "GSM3424990: IWR 1 rep2; Danio rerio; RNA Seq", "GSM3424990", null, "1", "Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank's Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 \u00b0C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80\u00b0C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.", "GEO Accession:GSM3424990", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP164769", null, null, "vanHollebeke_IWR_3_R1.fastq.gz", "fastq", 2320219813.0, 31532406.0, "GSM3424990 r1", "0:73.58 1:0", "A:660022378;C:501448817;G:498586533;T:660148405;N:13680", 73, 0, null, null, 660022378, 501448817, 498586533, 660148405, 13680, "SRX4820830", "SRS3895220", "SRA791232", "GEO", "MPI for heart and lung research", 1, 0.76766, null, 0.17893, null, 0.78206, null, 0.5236, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2018-10-09", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [49613, "SRR7989639", "SRX4820829", "SRS3895221", "SRP164769", "PRJNA495391", "Wnt/\u00df catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling", "GSE121041", "Transcriptome Analysis", "Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development  but also relevant for vascular and neurodegenerative diseases. However  beyond the early requirement of Wnt signaling for brain capillary development  there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation.  By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling  we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation.   In the absence of Wnt signaling  premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis  whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO", null, "pubmed:30451830;pubmed:38570687", null, "IWR 1 rep1", "GSM3424989", null, "source name:brain endothelial cells|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf", "IWR 1 rep1", "Raw reads were assessed for quality  adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene", "brain endothelial cells", null, "Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank\u2019s Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 \u00b0C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80\u00b0C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.", null, "lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf", "GSM3424989", "GSM3424989: IWR 1 rep1; Danio rerio; RNA Seq", "GSM3424989", null, "1", "Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank's Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 \u00b0C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80\u00b0C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.", "GEO Accession:GSM3424989", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP164769", null, null, "vanHollebeke_IWR_1_R1.fastq.gz", "fastq", 3130301804.0, 42242865.0, "GSM3424989 r1", "0:74.10 1:0", "A:906281071;C:658248293;G:654046147;T:911712569;N:13724", 74, 0, null, null, 906281071, 658248293, 654046147, 911712569, 13724, "SRX4820829", "SRS3895221", "SRA791232", "GEO", "MPI for heart and lung research", 1, 0.83335, null, 0.2301, null, 0.77703, null, 0.51424, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2018-10-09", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [49614, "SRR7989638", "SRX4820828", "SRS3895223", "SRP164769", "PRJNA495391", "Wnt/\u00df catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling", "GSE121041", "Transcriptome Analysis", "Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development  but also relevant for vascular and neurodegenerative diseases. However  beyond the early requirement of Wnt signaling for brain capillary development  there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation.  By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling  we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation.   In the absence of Wnt signaling  premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis  whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO", null, "pubmed:30451830;pubmed:38570687", null, "DMSO rep3", "GSM3424988", null, "source name:brain endothelial cells|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf", "DMSO rep3", "Raw reads were assessed for quality  adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene", "brain endothelial cells", null, "Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank\u2019s Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 \u00b0C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80\u00b0C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.", null, "lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf", "GSM3424988", "GSM3424988: DMSO rep3; Danio rerio; RNA Seq", "GSM3424988", null, "1", "Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank's Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 \u00b0C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80\u00b0C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.", "GEO Accession:GSM3424988", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP164769", null, null, "vanHollebeke_WT_3_R1.fastq.gz", "fastq", 2942028868.0, 39840018.0, "GSM3424988 r1", "0:73.85 1:0", "A:849808636;C:623040120;G:619275913;T:849871928;N:32271", 73, 0, null, null, 849808636, 623040120, 619275913, 849871928, 32271, "SRX4820828", "SRS3895223", "SRA791232", "GEO", "MPI for heart and lung research", 1, 0.83348, null, 0.20415, null, 0.79147, null, 0.51054, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2018-10-09", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [49615, "SRR7989637", "SRX4820827", "SRS3895219", "SRP164769", "PRJNA495391", "Wnt/\u00df catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling", "GSE121041", "Transcriptome Analysis", "Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development  but also relevant for vascular and neurodegenerative diseases. However  beyond the early requirement of Wnt signaling for brain capillary development  there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation.  By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling  we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation.   In the absence of Wnt signaling  premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis  whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO", null, "pubmed:30451830;pubmed:38570687", null, "DMSO rep2", "GSM3424987", null, "source name:brain endothelial cells|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf", "DMSO rep2", "Raw reads were assessed for quality  adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene", "brain endothelial cells", null, "Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank\u2019s Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 \u00b0C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80\u00b0C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.", null, "lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf", "GSM3424987", "GSM3424987: DMSO rep2; Danio rerio; RNA Seq", "GSM3424987", null, "1", "Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank's Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 \u00b0C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80\u00b0C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.", "GEO Accession:GSM3424987", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP164769", null, null, "vanHollebeke_WT_2_R1.fastq.gz", "fastq", 2807935583.0, 38002656.0, "GSM3424987 r1", "0:73.89 1:0", "A:815631502;C:589381721;G:586257915;T:816652021;N:12424", 73, 0, null, null, 815631502, 589381721, 586257915, 816652021, 12424, "SRX4820827", "SRS3895219", "SRA791232", "GEO", "MPI for heart and lung research", 1, 0.84347, null, 0.20267, null, 0.77419, null, 0.51656, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2018-10-09", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [49616, "SRR7989636", "SRX4820826", "SRS3895218", "SRP164769", "PRJNA495391", "Wnt/\u00df catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling", "GSE121041", "Transcriptome Analysis", "Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development  but also relevant for vascular and neurodegenerative diseases. However  beyond the early requirement of Wnt signaling for brain capillary development  there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation.  By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling  we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation.   In the absence of Wnt signaling  premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis  whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO", null, "pubmed:30451830;pubmed:38570687", null, "DMSO rep1", "GSM3424986", null, "source name:brain endothelial cells|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf", "DMSO rep1", "Raw reads were assessed for quality  adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene", "brain endothelial cells", null, "Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank\u2019s Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 \u00b0C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80\u00b0C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.", null, "lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf", "GSM3424986", "GSM3424986: DMSO rep1; Danio rerio; RNA Seq", "GSM3424986", null, "1", "Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank's Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 \u00b0C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80\u00b0C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.", "GEO Accession:GSM3424986", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP164769", null, null, "vanHollebeke_WT_1_R1.fastq.gz", "fastq", 2675908817.0, 36130876.0, "GSM3424986 r1", "0:74.06 1:0", "A:789957205;C:549799082;G:546545868;T:789594811;N:11851", 74, 0, null, null, 789957205, 549799082, 546545868, 789594811, 11851, "SRX4820826", "SRS3895218", "SRA791232", "GEO", "MPI for heart and lung research", 1, 0.90594, null, 0.2159, null, 0.76765, null, 0.50407, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2018-10-09", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [53493, "SRR9881612", "SRX6634133", "SRS5205093", "SRP217216", "PRJNA558070", "N Glycome regulation limits the transdifferentiation of endothelial cells into hematopoietic stem cells", "GSE135246", "Transcriptome Analysis", "Hematopoietic stem and progenitor cells HSPCs are required to establish and maintain the adult blood system in vertebrates. During development  HPSCs are generated from hemogenic endothelial cells that undergo an endothelial to hematopoietic transition EHT. Growth factors and epigenetic changes can promote EHT  but these mechanisms do not explain its tight spatiotemporal regulation during development. Here  we show that microRNA miR miR 223 mediated regulation of N glycan biosynthesis intrinsically restrains EHT  representing a new pathway that prevents excessive HSPC production. We find that miR 223 is uniquely expressed in hemogenic endothelial cells undergoing EHT and in nascent HSPCs. Loss of miR 223 promotes the expansion of these cells in the zebrafish and mouse aorta gonad mesonephros AGM  where EHT occurs. miR 223 targets alg2 alpha 1 3/ 1 6 mannosyltransferase in the AGM endothelium to restrict hemogenic and HSPC specification. This enzyme is involved in the attachment of the N glycans   a common co translational modification9 12 that influences several pathophysiological processes  but has not yet been implicated in EHT. Using an N glycosensor  we demonstrate that abundant protein N glycan attachment occurs in vascular cells during EHT  and this process is required for HSPC production. High throughput glycome analysis upon loss of miR 223 revealed that terminal alpha 1 3/6 mannose modifications are increased at the expense of alpha 2 3/6 sialic acid sugars. Importantly  pharmacological manipulation targeting these N glycan types in wild type embryos phenocopies the loss of miR 223 and enhances EHT as well as HSPC production. Thus  the N glycome plays a previously unappreciated role as an intrinsic regulator of EHT  with specific mannose and sialic acid modifications serving as key endothelial determinants to restrict the hematopoietic fate. Overall design: Single cell RNA sequencing for zebrafish Tgkdrl:hras mCherrys896 endothelial cells at 27 hpf for wildtype and miR 223ya303 backgrounds", null, "pubmed:33273096", null, "223mut 27hpf EC1", "GSM3996907", null, "source name:endothelial cell|tissue:trunk endothelium|cell type:endothelial cell|developmental stage:27 hpf 223:KalTA4ya363; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896; miR 223ya303|genotype:223mut", "223mut 27hpf EC1", "The reads were demultiplexed using bcl2fastq provided by the 10X genomics.  The demultiplexed reads were aligned to the reference genome Grz11  modified to add mCherry  GAL4  and eGFP to obtain digital gene expression matrix data using cellranger program The output of the cellranger was then processed using Seurat in R. All the cells with less than 200 unique transcripts were eliminared.  All genes which are expressed in less than 3 cells were also eliminated. The data was normalized using sctransform  and then clustered.  The clusters were projected for viualization in R using the PHATE algorithm. Genome build: GRCz11 Supplementary files format and content: Average Gene expression matrix for average gene expression per cluster  per condition.  This is a tab separated values file  where each row represents a gene  and each column represents the cluster  and the condition  and each cell represents normalized expression values across all the cells in that cluster for that condition.", "endothelial cell", null, "Trunk tissue was dissected from 27 hpf zebrafish embryos under  0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell 3\u2019 Library Construction Kit v2.1", "Zebrafish were raised and maintained at 28.5\u02daC using standard methods and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2017 11473.", "tissue:trunk endothelium|cell type:endothelial cell|developmental stage:27 hpf 223:KalTA4ya363; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896; miR 223ya303|genotype:223mut", "GSM3996907", "GSM3996907: 223mut 27hpf EC1; Danio rerio; RNA Seq", "GSM3996907", null, "1", "Trunk tissue was dissected from 27 hpf zebrafish embryos under  0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell three prime Library Construction Kit v2.1", "GEO Accession:GSM3996907", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP217216", null, null, "Mut_pssorted_genome_bam.bam", "10X Genomics bam file", 31174899854.0, 318111223.0, "GSM3996907 r1", "0:98", "A:8464403532;C:7291172763;G:7282393533;T:8131647604;N:5282422", 98, null, null, null, 8464403532, 7291172763, 7282393533, 8131647604, 5282422, "SRX6634133", "SRS5205093", "SRA930499", "GEO", "Internal Medicine, Yale University", 1, 0.92745, null, 0.05306, null, 0.84502, null, 0.46383, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-08-01", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [53494, "SRR9881611", "SRX6634132", "SRS5205092", "SRP217216", "PRJNA558070", "N Glycome regulation limits the transdifferentiation of endothelial cells into hematopoietic stem cells", "GSE135246", "Transcriptome Analysis", "Hematopoietic stem and progenitor cells HSPCs are required to establish and maintain the adult blood system in vertebrates. During development  HPSCs are generated from hemogenic endothelial cells that undergo an endothelial to hematopoietic transition EHT. Growth factors and epigenetic changes can promote EHT  but these mechanisms do not explain its tight spatiotemporal regulation during development. Here  we show that microRNA miR miR 223 mediated regulation of N glycan biosynthesis intrinsically restrains EHT  representing a new pathway that prevents excessive HSPC production. We find that miR 223 is uniquely expressed in hemogenic endothelial cells undergoing EHT and in nascent HSPCs. Loss of miR 223 promotes the expansion of these cells in the zebrafish and mouse aorta gonad mesonephros AGM  where EHT occurs. miR 223 targets alg2 alpha 1 3/ 1 6 mannosyltransferase in the AGM endothelium to restrict hemogenic and HSPC specification. This enzyme is involved in the attachment of the N glycans   a common co translational modification9 12 that influences several pathophysiological processes  but has not yet been implicated in EHT. Using an N glycosensor  we demonstrate that abundant protein N glycan attachment occurs in vascular cells during EHT  and this process is required for HSPC production. High throughput glycome analysis upon loss of miR 223 revealed that terminal alpha 1 3/6 mannose modifications are increased at the expense of alpha 2 3/6 sialic acid sugars. Importantly  pharmacological manipulation targeting these N glycan types in wild type embryos phenocopies the loss of miR 223 and enhances EHT as well as HSPC production. Thus  the N glycome plays a previously unappreciated role as an intrinsic regulator of EHT  with specific mannose and sialic acid modifications serving as key endothelial determinants to restrict the hematopoietic fate. Overall design: Single cell RNA sequencing for zebrafish Tgkdrl:hras mCherrys896 endothelial cells at 27 hpf for wildtype and miR 223ya303 backgrounds", null, "pubmed:33273096", null, "wildtype 27hpf EC1", "GSM3996906", null, "source name:endothelial cell|tissue:trunk endothelium|cell type:endothelial cell|developmental stage:27 hpf 223:KalTA4ya362; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896|genotype:wildtype", "wildtype 27hpf EC1", "The reads were demultiplexed using bcl2fastq provided by the 10X genomics.  The demultiplexed reads were aligned to the reference genome Grz11  modified to add mCherry  GAL4  and eGFP to obtain digital gene expression matrix data using cellranger program The output of the cellranger was then processed using Seurat in R. All the cells with less than 200 unique transcripts were eliminared.  All genes which are expressed in less than 3 cells were also eliminated. The data was normalized using sctransform  and then clustered.  The clusters were projected for viualization in R using the PHATE algorithm. Genome build: GRCz11 Supplementary files format and content: Average Gene expression matrix for average gene expression per cluster  per condition.  This is a tab separated values file  where each row represents a gene  and each column represents the cluster  and the condition  and each cell represents normalized expression values across all the cells in that cluster for that condition.", "endothelial cell", null, "Trunk tissue was dissected from 27 hpf zebrafish embryos under  0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell 3\u2019 Library Construction Kit v2.1", "Zebrafish were raised and maintained at 28.5\u02daC using standard methods and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2017 11473.", "tissue:trunk endothelium|cell type:endothelial cell|developmental stage:27 hpf 223:KalTA4ya362; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896|genotype:wildtype", "GSM3996906", "GSM3996906: wildtype 27hpf EC1; Danio rerio; RNA Seq", "GSM3996906", null, "1", "Trunk tissue was dissected from 27 hpf zebrafish embryos under  0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell three prime Library Construction Kit v2.1", "GEO Accession:GSM3996906", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP217216", null, null, "WT_pssorted_genome_bam.bam", "10X Genomics bam file", 26866951370.0, 274152565.0, "GSM3996906 r1", "0:98", "A:7373453026;C:6169004304;G:6196779570;T:7121490110;N:6224360", 98, null, null, null, 7373453026, 6169004304, 6196779570, 7121490110, 6224360, "SRX6634132", "SRS5205092", "SRA930499", "GEO", "Internal Medicine, Yale University", 1, 0.93015, null, 0.0602, null, 0.83853, null, 0.4683, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-08-01", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [53504, "SRR9879915", "SRX6632436", "SRS5202043", "SRP217196", "PRJNA558085", "Zebrafish Danio rerio neural crest cell RNA sequencing", "GSE135237", "Transcriptome Analysis", "RNA sequencing of neural crest cells collected from Gtfoxd3:mCherry;Tgsox10:mEGFP embryos Overall design: foxd3+/sox10+ double positive neural crest cells NCC were collected from the trunk of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos at 36 hpf and 72 hpf and sent for sequencing. 3 replicates for each condition.", null, "pubmed:31495570", null, "36hpfNCC rep3", "GSM3996851", null, "source name:Neural crest cells from larval trunk|tissue:Neural crest cells from larval trunk|transgene:Gtfoxd3:mCherry|transgene:Tgsox10:mEGFP|Stage:36 hpf", "36hpfNCC rep3", "For data quality control  FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping  we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5\u2032 to 3\u2032 and removes bases only at the 3\u2032 end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20  the 3\u2032 end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations", "Neural crest cells from larval trunk", "36 hpf and 72 hpf Gtfoxd3:mCherry;Tgsox10:mEGFP embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer\u2019s solution with 2.5mM EDTA and rocked for 15 minutes at 4 \u00b0C. The trunk pieces were washed three times with chilled Dulbecco\u2019s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 \u00b0C  1ml 1x Trypsin with 5% EDTA solution was added  and the samples were incubated for 15 more minutes at 28.5 \u00b0C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 \u03bcm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 \u00b1 750 at each stage were used for RNA sequencing.", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "Gtfoxd3:mCherry;Tgsox10:mEGFP zebrafish embryos were raised in egg water at 28.5C to desired stages", "tissue:Neural crest cells from larval trunk|transgene:Gtfoxd3:mCherry|transgene:Tgsox10:mEGFP|Stage:36 hpf", "GSM3996851", "GSM3996851: 36hpfNCC rep3; Danio rerio; RNA Seq", "GSM3996851", null, "1", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "GEO Accession:GSM3996851", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP217196", null, null, "Sample3_S3_R1_001.fastq.gz Sample3_S3_R2_001.fastq.gz", "fastq fastq", 5670363307.0, 19001526.0, "GSM3996851 r1", "0:149.23 1:149.19", "A:1557295113;C:1251445377;G:1252062318;T:1609175566;N:384933", 149, 149, null, null, 1557295113, 1251445377, 1252062318, 1609175566, 384933, "SRX6632436", "SRS5202043", "SRA930488", "GEO", "Kucenas Lab, Biology, University of Virginia", 2, 0.85581, 0.858, 0.14092, 0.14122, 0.78784, 0.7935, 0.55466, 0.55065, 150, 149, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2019-08-01", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [53505, "SRR9879914", "SRX6632435", "SRS5202042", "SRP217196", "PRJNA558085", "Zebrafish Danio rerio neural crest cell RNA sequencing", "GSE135237", "Transcriptome Analysis", "RNA sequencing of neural crest cells collected from Gtfoxd3:mCherry;Tgsox10:mEGFP embryos Overall design: foxd3+/sox10+ double positive neural crest cells NCC were collected from the trunk of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos at 36 hpf and 72 hpf and sent for sequencing. 3 replicates for each condition.", null, "pubmed:31495570", null, "36hpfNCC rep2", "GSM3996850", null, "source name:Neural crest cells from larval trunk|tissue:Neural crest cells from larval trunk|transgene:Gtfoxd3:mCherry|transgene:Tgsox10:mEGFP|Stage:36 hpf", "36hpfNCC rep2", "For data quality control  FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping  we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5\u2032 to 3\u2032 and removes bases only at the 3\u2032 end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20  the 3\u2032 end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations", "Neural crest cells from larval trunk", "36 hpf and 72 hpf Gtfoxd3:mCherry;Tgsox10:mEGFP embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer\u2019s solution with 2.5mM EDTA and rocked for 15 minutes at 4 \u00b0C. The trunk pieces were washed three times with chilled Dulbecco\u2019s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 \u00b0C  1ml 1x Trypsin with 5% EDTA solution was added  and the samples were incubated for 15 more minutes at 28.5 \u00b0C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 \u03bcm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 \u00b1 750 at each stage were used for RNA sequencing.", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "Gtfoxd3:mCherry;Tgsox10:mEGFP zebrafish embryos were raised in egg water at 28.5C to desired stages", "tissue:Neural crest cells from larval trunk|transgene:Gtfoxd3:mCherry|transgene:Tgsox10:mEGFP|Stage:36 hpf", "GSM3996850", "GSM3996850: 36hpfNCC rep2; Danio rerio; RNA Seq", "GSM3996850", null, "1", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "GEO Accession:GSM3996850", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP217196", null, null, "Sample2_S2_R2_001.fastq.gz Sample2_S2_R1_001.fastq.gz", "fastq fastq", 7936706863.0, 26647099.0, "GSM3996850 r1", "0:148.93 1:148.91", "A:2180170247;C:1758018091;G:1758076526;T:2239839139;N:602860", 148, 148, null, null, 2180170247, 1758018091, 1758076526, 2239839139, 602860, "SRX6632435", "SRS5202042", "SRA930488", "GEO", "Kucenas Lab, Biology, University of Virginia", 2, 0.85787, 0.85726, 0.14387, 0.14335, 0.7864, 0.79123, 0.55424, 0.54305, 150, 149, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2019-08-01", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"], [53506, "SRR9879913", "SRX6632434", "SRS5202041", "SRP217196", "PRJNA558085", "Zebrafish Danio rerio neural crest cell RNA sequencing", "GSE135237", "Transcriptome Analysis", "RNA sequencing of neural crest cells collected from Gtfoxd3:mCherry;Tgsox10:mEGFP embryos Overall design: foxd3+/sox10+ double positive neural crest cells NCC were collected from the trunk of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos at 36 hpf and 72 hpf and sent for sequencing. 3 replicates for each condition.", null, "pubmed:31495570", null, "36hpfNCC rep1", "GSM3996849", null, "source name:Neural crest cells from larval trunk|tissue:Neural crest cells from larval trunk|transgene:Gtfoxd3:mCherry|transgene:Tgsox10:mEGFP|Stage:36 hpf", "36hpfNCC rep1", "For data quality control  FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping  we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5\u2032 to 3\u2032 and removes bases only at the 3\u2032 end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20  the 3\u2032 end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations", "Neural crest cells from larval trunk", "36 hpf and 72 hpf Gtfoxd3:mCherry;Tgsox10:mEGFP embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer\u2019s solution with 2.5mM EDTA and rocked for 15 minutes at 4 \u00b0C. The trunk pieces were washed three times with chilled Dulbecco\u2019s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 \u00b0C  1ml 1x Trypsin with 5% EDTA solution was added  and the samples were incubated for 15 more minutes at 28.5 \u00b0C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 \u03bcm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 \u00b1 750 at each stage were used for RNA sequencing.", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "Gtfoxd3:mCherry;Tgsox10:mEGFP zebrafish embryos were raised in egg water at 28.5C to desired stages", "tissue:Neural crest cells from larval trunk|transgene:Gtfoxd3:mCherry|transgene:Tgsox10:mEGFP|Stage:36 hpf", "GSM3996849", "GSM3996849: 36hpfNCC rep1; Danio rerio; RNA Seq", "GSM3996849", null, "1", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "GEO Accession:GSM3996849", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP217196", null, null, "Sample1_S1_R1_001.fastq.gz Sample1_S1_R2_001.fastq.gz", "fastq fastq", 5567367667.0, 18627261.0, "GSM3996849 r1", "0:149.46 1:149.42", "A:1451891750;C:1299527629;G:1299734297;T:1515800229;N:413762", 149, 149, null, null, 1451891750, 1299527629, 1299734297, 1515800229, 413762, "SRX6632434", "SRS5202041", "SRA930488", "GEO", "Kucenas Lab, Biology, University of Virginia", 2, 0.70717, 0.70612, 0.10919, 0.10754, 0.83366, 0.83875, 0.55253, 0.55519, 149, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2019-08-01", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"]], "truncated": false, "filtered_table_rows_count": 210, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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], 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