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
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.,,,natural paring early sample,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate2],SAMD00073604,,sample name:M 4th|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073604,DRX078028,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate2],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073604,,,,1389837888.0,38606608.0,DRR084197,0:36,A:320671418;C:336948866;G:347550258;T:381720581;N:2946765,36,,,,320671418,336948866,347550258,381720581,2946765,DRX078028,DRS086522,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.89763,,0.02235,,0.76445,,0.46381,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Zygote,Embryo,Multi-tissue,Multi-system
181,DRR084191,DRX078022,DRS086516,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.,,,natural paring early sample,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate1],SAMD00073598,,sample name:M|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073598,DRX078022,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate1],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073598,,,,1050981012.0,29193917.0,DRR084191,0:36,A:241048832;C:256186268;G:260277071;T:293299597;N:169244,36,,,,241048832,256186268,260277071,293299597,169244,DRX078022,DRS086516,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.9088,,0.02369,,0.7624,,0.47998,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Zygote,Embryo,Multi-tissue,Multi-system
10188,ERR600685,ERX557514,ERS460539,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.,,,,,SAMEA2537630,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:SAMEA2537630|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 TC9 WT F sc 1951842|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. 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,,,,,,,,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,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,,,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,,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.,,,,,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,,,,,,,,,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.  This submission includes reads tagged with the sequence TTCCATTG.,qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP003932,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16,13129_8#8.cram,cram,1995224064.0,15587688.0,SC RUN 13129 8#8,0:53 1:75,A:508909383;C:332355977;G:373835062;T:775089830;N:5033812,53,75,,,508909383,332355977,373835062,775089830,5033812,ERX557513,ERS460538,ERA358077,SC,Wellcome Sanger Institute,2,0.31242,0.8426,0.16835,0.02824,0.96921,0.81606,0.27677,0.49882,53,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2014-09-16,Zygote,Embryo,Multi-tissue,Multi-system
10190,ERR600683,ERX557512,ERS460537,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.,,,,,SAMEA2537628,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 08T17:57:23Z|External Id:SAMEA2537628|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 TC7 buc 3 sc 1951840|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. 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,,,,,,,,,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.  This submission includes reads tagged with the sequence TAGTCTTG.,qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP003932,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16,13129_8#7.cram,cram,1335316864.0,10432163.0,SC RUN 13129 8#7,0:53 1:75,A:318582120;C:238156133;G:258642941;T:516548945;N:3386725,53,75,,,318582120,238156133,258642941,516548945,3386725,ERX557512,ERS460537,ERA358077,SC,Wellcome Sanger Institute,2,0.32517,0.89235,0.16229,0.04485,0.97634,0.90057,0.32073,0.47925,53,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2014-09-16,Zygote,Embryo,Multi-tissue,Multi-system
10191,ERR600682,ERX557511,ERS460536,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.,,,,,SAMEA2537627,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 08T17:42:28Z|External Id:SAMEA2537627|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 TC6 buc 2 sc 1951839|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. 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,,,,,,,,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,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,,,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,,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.,,,,,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. A 10 base indexing sequence TCCTCAATAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC5 buc 1 sc 1951838|scientific name:Danio rerio|strain:AB,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 13129 8#5,10325314,Illumina sequencing of library 10325314  constructed from sample accession ERS460535 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13129 8.  This submission includes reads tagged with the sequence TCCTCAAT.,qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,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,,,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,,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.,,,,,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. A 10 base indexing sequence TACAGGATAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC4 Tg 1 sc 1951837|scientific name:Danio rerio|strain:AB,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 13129 8#4,10325313,Illumina sequencing of library 10325313  constructed from sample accession ERS460534 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13129 8.  This submission includes reads tagged with the sequence TACAGGAT.,qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,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,,,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,,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.,,,,,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,,,,,,,,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,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,,,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,,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.,,,,,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,,,,,,,,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,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,,,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,,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.,,,,,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,,,,,,,,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,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,,,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,,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.,,,,,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,,,,,,,,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,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,,,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,,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.,,,,,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,,,,,,,,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,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,,,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,,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.,,,,,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,,,,,,,,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,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,,,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,,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.,,,,,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,,,,,,,,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,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,,,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,,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.,,,,,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,,,,,,,,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,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,,,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,,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.,,,,,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,,,,,,,,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,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,,,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,,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.,,,,,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,,,,,,,,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,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,,,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,,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.,,,,,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,,,,,,,,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,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,,,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,,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.,,,,,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,,,,,,,,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,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,,,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,,United Kingdom,2014-09-09,Zygote,Embryo,Multi-tissue,Multi-system
24838,SRR25509990,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S65_L001_I1_001.fastq.gz Kristen_10X_101620_S65_L001_R1_001.fastq.gz Kristen_10X_101620_S65_L001_R2_001.fastq.gz,fastq fastq fastq,3327423622.0,26200186.0,GSM7680082 r1,0:8 1:28 2:91,A:693698335;C:494975421;G:540414923;T:654926705;N:201542,8,28,91,,693698335,494975421,540414923,654926705,201542,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91351,,0.22865,,0.77723,,0.49805,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24839,SRR25509991,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S67_L002_I1_001.fastq.gz Kristen_10X_101620_S67_L002_R1_001.fastq.gz Kristen_10X_101620_S67_L002_R2_001.fastq.gz,fastq fastq fastq,4430975390.0,34889570.0,GSM7680082 r10,0:8 1:28 2:91,A:923557751;C:658731986;G:718325003;T:874072049;N:264081,8,28,91,,923557751,658731986,718325003,874072049,264081,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91797,,0.22868,,0.77863,,0.50737,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24840,SRR25509992,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S67_L003_I1_001.fastq.gz Kristen_10X_101620_S67_L003_R1_001.fastq.gz Kristen_10X_101620_S67_L003_R2_001.fastq.gz,fastq fastq fastq,4429223552.0,34875776.0,GSM7680082 r11,0:8 1:28 2:91,A:923277621;C:658440918;G:718036099;T:873676803;N:264175,8,28,91,,923277621,658440918,718036099,873676803,264175,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91753,,0.22978,,0.77942,,0.50977,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24841,SRR25509993,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S67_L004_I1_001.fastq.gz Kristen_10X_101620_S67_L004_R1_001.fastq.gz Kristen_10X_101620_S67_L004_R2_001.fastq.gz,fastq fastq fastq,4549656890.0,35824070.0,GSM7680082 r12,0:8 1:28 2:91,A:950423951;C:673969790;G:734760168;T:900554096;N:282365,8,28,91,,950423951,673969790,734760168,900554096,282365,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91687,,0.23323,,0.77932,,0.50984,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24842,SRR25509994,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S68_L001_I1_001.fastq.gz Kristen_10X_101620_S68_L001_R1_001.fastq.gz Kristen_10X_101620_S68_L001_R2_001.fastq.gz,fastq fastq fastq,2696456634.0,21231942.0,GSM7680082 r13,0:8 1:28 2:91,A:562209710;C:401113540;G:437836456;T:530785441;N:161575,8,28,91,,562209710,401113540,437836456,530785441,161575,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91384,,0.22885,,0.77912,,0.50672,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24843,SRR25509995,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S68_L002_I1_001.fastq.gz Kristen_10X_101620_S68_L002_R1_001.fastq.gz Kristen_10X_101620_S68_L002_R2_001.fastq.gz,fastq fastq fastq,2735162932.0,21536716.0,GSM7680082 r14,0:8 1:28 2:91,A:570169460;C:406846839;G:443964376;T:538696359;N:164122,8,28,91,,570169460,406846839,443964376,538696359,164122,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91691,,0.22998,,0.77942,,0.51035,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24844,SRR25509996,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S68_L003_I1_001.fastq.gz Kristen_10X_101620_S68_L003_R1_001.fastq.gz Kristen_10X_101620_S68_L003_R2_001.fastq.gz,fastq fastq fastq,2739703563.0,21572469.0,GSM7680082 r15,0:8 1:28 2:91,A:571283074;C:407511119;G:444574049;T:539563747;N:162690,8,28,91,,571283074,407511119,444574049,539563747,162690,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91526,,0.22747,,0.7793,,0.51387,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24845,SRR25509997,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S68_L004_I1_001.fastq.gz Kristen_10X_101620_S68_L004_R1_001.fastq.gz Kristen_10X_101620_S68_L004_R2_001.fastq.gz,fastq fastq fastq,2828960433.0,22275279.0,GSM7680082 r16,0:8 1:28 2:91,A:591166850;C:419193897;G:457332081;T:559181603;N:175958,8,28,91,,591166850,419193897,457332081,559181603,175958,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91651,,0.23126,,0.77613,,0.50223,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24846,SRR25509998,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S65_L002_I1_001.fastq.gz Kristen_10X_101620_S65_L002_R1_001.fastq.gz Kristen_10X_101620_S65_L002_R2_001.fastq.gz,fastq fastq fastq,3374189340.0,26568420.0,GSM7680082 r2,0:8 1:28 2:91,A:703424426;C:501911907;G:547786373;T:664402117;N:201397,8,28,91,,703424426,501911907,547786373,664402117,201397,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91522,,0.22812,,0.77753,,0.50208,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24847,SRR25509999,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S65_L003_I1_001.fastq.gz Kristen_10X_101620_S65_L003_R1_001.fastq.gz Kristen_10X_101620_S65_L003_R2_001.fastq.gz,fastq fastq fastq,3383217516.0,26639508.0,GSM7680082 r3,0:8 1:28 2:91,A:705514047;C:503189161;G:549089218;T:666200894;N:201908,8,28,91,,705514047,503189161,549089218,666200894,201908,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91535,,0.23036,,0.78078,,0.50202,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24848,SRR25510000,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S65_L004_I1_001.fastq.gz Kristen_10X_101620_S65_L004_R1_001.fastq.gz Kristen_10X_101620_S65_L004_R2_001.fastq.gz,fastq fastq fastq,3493154050.0,27505150.0,GSM7680082 r4,0:8 1:28 2:91,A:729910298;C:517582902;G:564926384;T:690333365;N:215701,8,28,91,,729910298,517582902,564926384,690333365,215701,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91569,,0.22913,,0.77873,,0.50186,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24849,SRR25510001,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S66_L001_I1_001.fastq.gz Kristen_10X_101620_S66_L001_R1_001.fastq.gz Kristen_10X_101620_S66_L001_R2_001.fastq.gz,fastq fastq fastq,3237456187.0,25491781.0,GSM7680082 r5,0:8 1:28 2:91,A:674885196;C:481871349;G:525642933;T:637154812;N:197781,8,28,91,,674885196,481871349,525642933,637154812,197781,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91378,,0.22852,,0.77843,,0.50985,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24850,SRR25510002,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S66_L002_I1_001.fastq.gz Kristen_10X_101620_S66_L002_R1_001.fastq.gz Kristen_10X_101620_S66_L002_R2_001.fastq.gz,fastq fastq fastq,3287789081.0,25888103.0,GSM7680082 r6,0:8 1:28 2:91,A:685408765;C:489232060;G:533550966;T:647427897;N:197685,8,28,91,,685408765,489232060,533550966,647427897,197685,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91484,,0.22872,,0.78001,,0.49909,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24851,SRR25510003,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S66_L003_I1_001.fastq.gz Kristen_10X_101620_S66_L003_R1_001.fastq.gz Kristen_10X_101620_S66_L003_R2_001.fastq.gz,fastq fastq fastq,3298207145.0,25970135.0,GSM7680082 r7,0:8 1:28 2:91,A:687621787;C:490851045;G:535230137;T:649382247;N:197069,8,28,91,,687621787,490851045,535230137,649382247,197069,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91559,,0.2268,,0.77766,,0.50935,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24852,SRR25510004,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S66_L004_I1_001.fastq.gz Kristen_10X_101620_S66_L004_R1_001.fastq.gz Kristen_10X_101620_S66_L004_R2_001.fastq.gz,fastq fastq fastq,3377888088.0,26597544.0,GSM7680082 r8,0:8 1:28 2:91,A:705624374;C:500985504;G:546306692;T:667248332;N:211602,8,28,91,,705624374,500985504,546306692,667248332,211602,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91679,,0.22965,,0.77837,,0.51495,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24853,SRR25510005,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S67_L001_I1_001.fastq.gz Kristen_10X_101620_S67_L001_R1_001.fastq.gz Kristen_10X_101620_S67_L001_R2_001.fastq.gz,fastq fastq fastq,4346114117.0,34221371.0,GSM7680082 r9,0:8 1:28 2:91,A:905838814;C:646261347;G:704993570;T:856789016;N:262014,8,28,91,,905838814,646261347,704993570,856789016,262014,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91558,,0.22834,,0.7783,,0.49972,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,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.,,pubmed:38742432,,EC  tie1 Homo  replicate 2  RNAseq,GSM7696246,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,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,,,,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,,0.67481,,0.78062,,0.49002,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,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.,,pubmed:38742432,,EC  tie1 Homo  replicate 2  RNAseq,GSM7696246,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,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,,,,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,,0.67543,,0.77796,,0.494,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,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.,,pubmed:38742432,,EC  tie1 Homo  replicate 2  RNAseq,GSM7696246,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,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,,,,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,,0.67812,,0.78255,,0.49198,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,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.,,pubmed:38742432,,EC  tie1 Homo  replicate 2  RNAseq,GSM7696246,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,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,,,,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,,0.67763,,0.78074,,0.49757,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,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.,,pubmed:38742432,,EC  tie1 Homo  replicate 1  RNAseq,GSM7696245,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,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,,,,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,,0.65866,,0.76238,,0.48958,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,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.,,pubmed:38742432,,EC  tie1 Homo  replicate 1  RNAseq,GSM7696245,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,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,,,,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,,0.65728,,0.76132,,0.4958,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,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.,,pubmed:38742432,,EC  tie1 Homo  replicate 1  RNAseq,GSM7696245,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,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,,,,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,,0.65858,,0.76177,,0.48634,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,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.,,pubmed:38742432,,EC  tie1 Homo  replicate 1  RNAseq,GSM7696245,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,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,,,,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,,0.66467,,0.76081,,0.49407,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,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.,,pubmed:38742432,,EC  tie1 WT/Het  replicate 2  RNAseq,GSM7696244,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,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,,,,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,,0.59772,,0.73553,,0.48949,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,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.,,pubmed:38742432,,EC  tie1 WT/Het  replicate 2  RNAseq,GSM7696244,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,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,,,,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,,0.59517,,0.73547,,0.48651,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,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.,,pubmed:38742432,,EC  tie1 WT/Het  replicate 2  RNAseq,GSM7696244,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,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,,,,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,,0.59465,,0.7359,,0.48952,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,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.,,pubmed:38742432,,EC  tie1 WT/Het  replicate 2  RNAseq,GSM7696244,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,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,,,,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,,0.59613,,0.73608,,0.48475,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,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.,,pubmed:38742432,,EC  tie1 WT/Het  replicate 1  RNAseq,GSM7696243,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,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,,,,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,,0.52962,,0.7349,,0.48594,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,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.,,pubmed:38742432,,EC  tie1 WT/Het  replicate 1  RNAseq,GSM7696243,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,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,,,,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,,0.52938,,0.73304,,0.48118,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,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.,,pubmed:38742432,,EC  tie1 WT/Het  replicate 1  RNAseq,GSM7696243,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,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,,,,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,,0.52836,,0.73419,,0.48215,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,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.,,pubmed:38742432,,EC  tie1 WT/Het  replicate 1  RNAseq,GSM7696243,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,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,,,,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,,0.52541,,0.73484,,0.48813,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,Japan,2023-08-08,Pharyngula,Embryo,Multi-tissue,Multi-system
25133,SRR25634296,SRX21361065,SRS18605555,SRP454944,PRJNA1005241,Nkx2.7 is a Conserved Regulator of Craniofacial Development,GSE240780,Transcriptome Analysis,Pharyngeal arch cells are comprised of endoderm  mesoderm  and neural crest layers. We used single cell RNA sequencing scRNA seq to analyze the genetic differences in pharyngeal arch cell types between wild type and nkx2.7 /  samples. Overall design: Pharyngeal arch cells were obtained through manual dissection of wild type and nkx2.7 /  embryos at 26 hpf. All embryos were positive for TgBACtcf21:mcherry NTR  which was used as a visual guide for dissection. Cells were FACS sorted to eliminate dead cells from sequencing. 2 wild type embryos and 2 nkx2.7 /  samples were pooled for submission.,,pubmed:40268889,,KC002  scRNAseq,GSM7709162,,source name:Pharyngeal arches|genotype:nkx2.7 / |tissue:Pharyngeal arches|strain:AB|developmental stage:26 hpf|geo loc name:missing|collection date:missing,KC002  scRNAseq,The read alignment and gene counting were made using the Cell Ranger software v6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 version 105 Supplementary files format and content: Tab separated values files and matrix files,Pharyngeal arches,,From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108  two wild type and two nkx2.7 /  embryos were identified by genotyping.  The pharyngeal arches and surrounding tissue were dissected  dissociated  and submitted for flow cytometry.  Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution.  Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C.  The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer.  Finally  DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI.  NERL Diluent 2 Thermo Fisher  DIL5522 solution was used for sheath fluid.  The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences  655051  SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m  5 mL Spherotech  RCP 30 5A  followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences  345249. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,genotype:nkx2.7 / |tissue:Pharyngeal arches|strain:AB|developmental stage:26 hpf,GSM7709162,GSM7709162: KC002  scRNAseq; Danio rerio; RNA Seq,GSM7709162 r1,GSM7709162,1,From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108  two wild type and two nkx2.7 /  embryos were identified by genotyping.  The pharyngeal arches and surrounding tissue were dissected  dissociated  and submitted for flow cytometry.  Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution.  Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C.  The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer.  Finally  DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI.  NERL Diluent 2 Thermo Fisher  DIL5522 solution was used for sheath fluid.  The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences  655051  SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m  5 mL Spherotech  RCP 30 5A  followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences  345249. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454944,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=KC002 S1 L004 I1 001.fastq.gz   read2PairFiles=KC002 S1 L004 I2 001.fastq.gz   read3PairFiles=KC002 S1 L004 R1 001.fastq.gz   read4PairFiles=KC002 S1 L004 R2 001.fastq.gz,KC002_S1_L004_I1_001.fastq.gz KC002_S1_L004_I2_001.fastq.gz KC002_S1_L004_R1_001.fastq.gz KC002_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,65825988564.0,296513462.0,GSM7709162 r1,0:10 1:10 2:101 3:101,A:14990994149;C:11485312838;G:11921291570;T:21497933732;N:187035,10,10,101,101,14990994149,11485312838,11921291570,21497933732,187035,SRX21361065,SRS18605555,SRA1692494,"SangesLab Computational Genomics, NEUROSCIENCE, SISSA","SangesLab Computational Genomics, NEUROSCIENCE, SISSA",2,0.00059,0.93473,2e-05,0.14487,0.99949,0.78364,0.5,0.52799,101,101,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Italy,2023-08-14,Pharyngula,Embryo,Pharyngeal Arch,Multi-system
25134,SRR25634297,SRX21361064,SRS18605556,SRP454944,PRJNA1005241,Nkx2.7 is a Conserved Regulator of Craniofacial Development,GSE240780,Transcriptome Analysis,Pharyngeal arch cells are comprised of endoderm  mesoderm  and neural crest layers. We used single cell RNA sequencing scRNA seq to analyze the genetic differences in pharyngeal arch cell types between wild type and nkx2.7 /  samples. Overall design: Pharyngeal arch cells were obtained through manual dissection of wild type and nkx2.7 /  embryos at 26 hpf. All embryos were positive for TgBACtcf21:mcherry NTR  which was used as a visual guide for dissection. Cells were FACS sorted to eliminate dead cells from sequencing. 2 wild type embryos and 2 nkx2.7 /  samples were pooled for submission.,,pubmed:40268889,,KC001  scRNAseq,GSM7709161,,source name:Pharyngeal arches|genotype:wild type|tissue:Pharyngeal arches|strain:AB|developmental stage:26 hpf|geo loc name:missing|collection date:missing,KC001  scRNAseq,The read alignment and gene counting were made using the Cell Ranger software v6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 version 105 Supplementary files format and content: Tab separated values files and matrix files,Pharyngeal arches,,From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108  two wild type and two nkx2.7 /  embryos were identified by genotyping.  The pharyngeal arches and surrounding tissue were dissected  dissociated  and submitted for flow cytometry.  Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution.  Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C.  The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer.  Finally  DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI.  NERL Diluent 2 Thermo Fisher  DIL5522 solution was used for sheath fluid.  The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences  655051  SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m  5 mL Spherotech  RCP 30 5A  followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences  345249. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,genotype:wild type|tissue:Pharyngeal arches|strain:AB|developmental stage:26 hpf,GSM7709161,GSM7709161: KC001  scRNAseq; Danio rerio; RNA Seq,GSM7709161 r1,GSM7709161,1,From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108  two wild type and two nkx2.7 /  embryos were identified by genotyping.  The pharyngeal arches and surrounding tissue were dissected  dissociated  and submitted for flow cytometry.  Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution.  Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C.  The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer.  Finally  DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI.  NERL Diluent 2 Thermo Fisher  DIL5522 solution was used for sheath fluid.  The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences  655051  SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m  5 mL Spherotech  RCP 30 5A  followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences  345249. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454944,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=KC001 S1 L004 I1 001.fastq.gz   read2PairFiles=KC001 S1 L004 I2 001.fastq.gz   read3PairFiles=KC001 S1 L004 R1 001.fastq.gz   read4PairFiles=KC001 S1 L004 R2 001.fastq.gz,KC001_S1_L004_I1_001.fastq.gz KC001_S1_L004_I2_001.fastq.gz KC001_S1_L004_R1_001.fastq.gz KC001_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,69380677872.0,312525576.0,GSM7709161 r1,0:10 1:10 2:101 3:101,A:16018222868;C:11704492905;G:12161620273;T:23245625739;N:204567,10,10,101,101,16018222868,11704492905,12161620273,23245625739,204567,SRX21361064,SRS18605556,SRA1692494,"SangesLab Computational Genomics, NEUROSCIENCE, SISSA","SangesLab Computational Genomics, NEUROSCIENCE, SISSA",2,0.00071,0.93976,0.0001,0.12725,0.99945,0.78457,0.75,0.50121,101,101,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Italy,2023-08-14,Pharyngula,Embryo,Pharyngeal Arch,Multi-system
28818,SRR26711836,SRX22410952,SRS19443730,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  Wnt stimulation  replicate 4,GSM7885889,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  Wnt stimulation  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885889,GSM7885889: rad21 heterozugous tailbud  Wnt stimulation  replicate 4; Danio rerio; RNA Seq,GSM7885889 r1,GSM7885889,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-8-HET_S32_L001_R2_001.fastq.gz Rad21-BIO-8-HET_S32_L001_R1_001.fastq.gz,fastq fastq,3261739218.0,21610373.0,GSM7885889 r1,0:75.52 1:75.42,A:816426262;C:810367718;G:804831968;T:829974289;N:138981,75,75,,,816426262,810367718,804831968,829974289,138981,SRX22410952,SRS19443730,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96738,0.97053,0.05473,0.05415,0.72283,0.72338,0.46691,0.46731,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28819,SRR26711837,SRX22410952,SRS19443730,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  Wnt stimulation  replicate 4,GSM7885889,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  Wnt stimulation  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885889,GSM7885889: rad21 heterozugous tailbud  Wnt stimulation  replicate 4; Danio rerio; RNA Seq,GSM7885889 r1,GSM7885889,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-8-HET_S32_L002_R2_001.fastq.gz Rad21-BIO-8-HET_S32_L002_R1_001.fastq.gz,fastq fastq,3279254436.0,21726495.0,GSM7885889 r2,0:75.52 1:75.42,A:821154343;C:814711347;G:809025779;T:834224252;N:138715,75,75,,,821154343,814711347,809025779,834224252,138715,SRX22410952,SRS19443730,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96764,0.97012,0.05449,0.05364,0.72362,0.72478,0.46065,0.44816,75,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28820,SRR26711838,SRX22410951,SRS19443729,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  Wnt stimulation  replicate 4,GSM7885888,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  Wnt stimulation  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885888,GSM7885888: rad21 homozygous tailbud  Wnt stimulation  replicate 4; Danio rerio; RNA Seq,GSM7885888 r1,GSM7885888,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-4-MUT_S31_L001_R1_001.fastq.gz Rad21-BIO-4-MUT_S31_L001_R2_001.fastq.gz,fastq fastq,3815700579.0,25275353.0,GSM7885888 r1,0:75.53 1:75.43,A:962537652;C:941667596;G:934433379;T:976947974;N:113978,75,75,,,962537652,941667596,934433379,976947974,113978,SRX22410951,SRS19443729,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96535,0.96731,0.06446,0.06372,0.71928,0.71956,0.47233,0.47166,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28821,SRR26711839,SRX22410951,SRS19443729,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  Wnt stimulation  replicate 4,GSM7885888,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  Wnt stimulation  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885888,GSM7885888: rad21 homozygous tailbud  Wnt stimulation  replicate 4; Danio rerio; RNA Seq,GSM7885888 r1,GSM7885888,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-4-MUT_S31_L002_R1_001.fastq.gz Rad21-BIO-4-MUT_S31_L002_R2_001.fastq.gz,fastq fastq,3837906036.0,25422663.0,GSM7885888 r2,0:75.53 1:75.43,A:968455256;C:947191550;G:939808490;T:982330983;N:119757,75,75,,,968455256,947191550,939808490,982330983,119757,SRX22410951,SRS19443729,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96615,0.96781,0.0624,0.06196,0.71725,0.71827,0.47042,0.46294,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28822,SRR26711840,SRX22410950,SRS19443727,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  no treatment  replicate 4,GSM7885887,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  no treatment  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant,GSM7885887,GSM7885887: rad21 heterozugous tailbud  no treatment  replicate 4; Danio rerio; RNA Seq,GSM7885887 r1,GSM7885887,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-8-HET_S30_L001_R2_001.fastq.gz Rad21-8-HET_S30_L001_R1_001.fastq.gz,fastq fastq,4150580457.0,27506773.0,GSM7885887 r1,0:75.51 1:75.39,A:1061191322;C:1016515755;G:1039117012;T:1033588629;N:167739,75,75,,,1061191322,1016515755,1039117012,1033588629,167739,SRX22410950,SRS19443727,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96699,0.96687,0.0501,0.04959,0.71642,0.72017,0.44914,0.44833,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28823,SRR26711841,SRX22410950,SRS19443727,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  no treatment  replicate 4,GSM7885887,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  no treatment  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant,GSM7885887,GSM7885887: rad21 heterozugous tailbud  no treatment  replicate 4; Danio rerio; RNA Seq,GSM7885887 r1,GSM7885887,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-8-HET_S30_L002_R2_001.fastq.gz Rad21-8-HET_S30_L002_R1_001.fastq.gz,fastq fastq,4170430033.0,27638560.0,GSM7885887 r2,0:75.50 1:75.39,A:1067297262;C:1021226653;G:1043544460;T:1038184807;N:176851,75,75,,,1067297262,1021226653,1043544460,1038184807,176851,SRX22410950,SRS19443727,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96619,0.96635,0.05062,0.05015,0.7139,0.71918,0.44965,0.45175,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28824,SRR26711842,SRX22410949,SRS19443728,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  no treatment  replicate 4,GSM7885886,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  no treatment  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant,GSM7885886,GSM7885886: rad21 homozygous tailbud  no treatment  replicate 4; Danio rerio; RNA Seq,GSM7885886 r1,GSM7885886,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-4-MUT_S29_L001_R1_001.fastq.gz Rad21-4-MUT_S29_L001_R2_001.fastq.gz,fastq fastq,3860758586.0,25585267.0,GSM7885886 r1,0:75.50 1:75.40,A:962978350;C:961963514;G:957530709;T:978120083;N:165930,75,75,,,962978350,961963514,957530709,978120083,165930,SRX22410949,SRS19443728,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96679,0.96899,0.05708,0.05592,0.71991,0.72021,0.44331,0.44736,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28825,SRR26711843,SRX22410949,SRS19443728,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  no treatment  replicate 4,GSM7885886,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  no treatment  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant,GSM7885886,GSM7885886: rad21 homozygous tailbud  no treatment  replicate 4; Danio rerio; RNA Seq,GSM7885886 r1,GSM7885886,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-4-MUT_S29_L002_R1_001.fastq.gz Rad21-4-MUT_S29_L002_R2_001.fastq.gz,fastq fastq,3886411017.0,25755387.0,GSM7885886 r2,0:75.50 1:75.40,A:969709828;C:968345638;G:963787543;T:984390915;N:177093,75,75,,,969709828,968345638,963787543,984390915,177093,SRX22410949,SRS19443728,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96682,0.96836,0.05697,0.05624,0.71812,0.71819,0.4505,0.44685,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28826,SRR26711844,SRX22410948,SRS19443726,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  Wnt stimulation  replicate 4,GSM7885885,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,stag2b tailbud  Wnt stimulation  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation,GSM7885885,GSM7885885: stag2b tailbud  Wnt stimulation  replicate 4; Danio rerio; RNA Seq,GSM7885885 r1,GSM7885885,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-BIO-4_S28_L001_R1_001.fastq.gz S2B-BIO-4_S28_L001_R2_001.fastq.gz,fastq fastq,3727162917.0,24693169.0,GSM7885885 r1,0:75.53 1:75.41,A:922580573;C:935922329;G:933433047;T:935120514;N:106454,75,75,,,922580573,935922329,933433047,935120514,106454,SRX22410948,SRS19443726,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96731,0.96936,0.04393,0.04403,0.72234,0.72397,0.46015,0.45955,76,74,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28827,SRR26711845,SRX22410948,SRS19443726,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  Wnt stimulation  replicate 4,GSM7885885,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,stag2b tailbud  Wnt stimulation  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation,GSM7885885,GSM7885885: stag2b tailbud  Wnt stimulation  replicate 4; Danio rerio; RNA Seq,GSM7885885 r1,GSM7885885,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-BIO-4_S28_L002_R1_001.fastq.gz S2B-BIO-4_S28_L002_R2_001.fastq.gz,fastq fastq,3749916462.0,24844024.0,GSM7885885 r2,0:75.53 1:75.41,A:928588967;C:941571510;G:939049263;T:940598432;N:108290,75,75,,,928588967,941571510,939049263,940598432,108290,SRX22410948,SRS19443726,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96668,0.96881,0.04401,0.04387,0.72387,0.72519,0.45814,0.457,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28828,SRR26711846,SRX22410947,SRS19443724,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  no treatment  replicate 4,GSM7885884,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing,stag2b tailbud  no treatment  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant,GSM7885884,GSM7885884: stag2b tailbud  no treatment  replicate 4; Danio rerio; RNA Seq,GSM7885884 r1,GSM7885884,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-4_S27_L001_R1_001.fastq.gz S2B-4_S27_L001_R2_001.fastq.gz,fastq fastq,4559287327.0,30217717.0,GSM7885884 r1,0:75.49 1:75.39,A:1129871064;C:1144626195;G:1141080047;T:1143531432;N:178589,75,75,,,1129871064,1144626195,1141080047,1143531432,178589,SRX22410947,SRS19443724,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96507,0.96728,0.04397,0.04385,0.72338,0.72456,0.44876,0.45623,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28829,SRR26711847,SRX22410947,SRS19443724,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  no treatment  replicate 4,GSM7885884,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing,stag2b tailbud  no treatment  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant,GSM7885884,GSM7885884: stag2b tailbud  no treatment  replicate 4; Danio rerio; RNA Seq,GSM7885884 r1,GSM7885884,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-4_S27_L002_R1_001.fastq.gz S2B-4_S27_L002_R2_001.fastq.gz,fastq fastq,4586674313.0,30399355.0,GSM7885884 r2,0:75.49 1:75.39,A:1137101056;C:1151500029;G:1147768493;T:1150129054;N:175681,75,75,,,1137101056,1151500029,1147768493,1150129054,175681,SRX22410947,SRS19443724,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96454,0.96735,0.04449,0.04408,0.72435,0.72583,0.45339,0.45434,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28830,SRR26711848,SRX22410946,SRS19443725,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  Wnt stimulation  replicate 4,GSM7885883,,source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,Wild type tailbud  Wnt stimulation  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation,GSM7885883,GSM7885883: Wild type tailbud  Wnt stimulation  replicate 4; Danio rerio; RNA Seq,GSM7885883 r1,GSM7885883,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT-BIO-4_S26_L001_R2_001.fastq.gz WT-BIO-4_S26_L001_R1_001.fastq.gz,fastq fastq,5251141754.0,34808166.0,GSM7885883 r1,0:75.48 1:75.38,A:1316653671;C:1303617399;G:1296205519;T:1334442750;N:222415,75,75,,,1316653671,1303617399,1296205519,1334442750,222415,SRX22410946,SRS19443725,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96497,0.96673,0.04868,0.04837,0.72332,0.72324,0.47006,0.45832,75,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28831,SRR26711849,SRX22410946,SRS19443725,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  Wnt stimulation  replicate 4,GSM7885883,,source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,Wild type tailbud  Wnt stimulation  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation,GSM7885883,GSM7885883: Wild type tailbud  Wnt stimulation  replicate 4; Danio rerio; RNA Seq,GSM7885883 r1,GSM7885883,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT-BIO-4_S26_L002_R2_001.fastq.gz WT-BIO-4_S26_L002_R1_001.fastq.gz,fastq fastq,5280302307.0,35001391.0,GSM7885883 r2,0:75.48 1:75.38,A:1324401398;C:1310930748;G:1303177704;T:1341576726;N:215731,75,75,,,1324401398,1310930748,1303177704,1341576726,215731,SRX22410946,SRS19443725,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96424,0.96713,0.04917,0.04864,0.72241,0.72271,0.46443,0.45274,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28832,SRR26711850,SRX22410945,SRS19443723,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  no treatment  replicate 4,GSM7885882,,source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing,Wild type tailbud  no treatment  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type,GSM7885882,GSM7885882: Wild type tailbud  no treatment  replicate 4; Danio rerio; RNA Seq,GSM7885882 r1,GSM7885882,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT4_S25_L001_R1_001.fastq.gz WT4_S25_L001_R2_001.fastq.gz,fastq fastq,7405469360.0,49089434.0,GSM7885882 r1,0:75.49 1:75.37,A:1847973647;C:1841169648;G:1840295933;T:1875743550;N:286582,75,75,,,1847973647,1841169648,1840295933,1875743550,286582,SRX22410945,SRS19443723,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96338,0.96738,0.04317,0.04296,0.71737,0.71851,0.45679,0.45543,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28833,SRR26711851,SRX22410945,SRS19443723,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  no treatment  replicate 4,GSM7885882,,source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing,Wild type tailbud  no treatment  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type,GSM7885882,GSM7885882: Wild type tailbud  no treatment  replicate 4; Danio rerio; RNA Seq,GSM7885882 r1,GSM7885882,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT4_S25_L002_R1_001.fastq.gz WT4_S25_L002_R2_001.fastq.gz,fastq fastq,7449020435.0,49378676.0,GSM7885882 r2,0:75.48 1:75.37,A:1859225781;C:1852173354;G:1850890621;T:1886441454;N:289225,75,75,,,1859225781,1852173354,1850890621,1886441454,289225,SRX22410945,SRS19443723,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96307,0.9662,0.04334,0.04269,0.7167,0.71679,0.45909,0.45956,75,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28834,SRR26711852,SRX22410944,SRS19443721,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  Wnt stimulation  replicate 3,GSM7885881,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  Wnt stimulation  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885881,GSM7885881: rad21 heterozugous tailbud  Wnt stimulation  replicate 3; Danio rerio; RNA Seq,GSM7885881 r1,GSM7885881,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-7-HET_S24_L001_R1_001.fastq.gz Rad21-BIO-7-HET_S24_L001_R2_001.fastq.gz,fastq fastq,3984218790.0,26397905.0,GSM7885881 r1,0:75.51 1:75.42,A:1024724878;C:960806363;G:958470013;T:1040115284;N:102252,75,75,,,1024724878,960806363,958470013,1040115284,102252,SRX22410944,SRS19443721,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95932,0.96163,0.06729,0.06702,0.71979,0.71981,0.4528,0.4607,76,74,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28835,SRR26711853,SRX22410944,SRS19443721,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  Wnt stimulation  replicate 3,GSM7885881,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  Wnt stimulation  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885881,GSM7885881: rad21 heterozugous tailbud  Wnt stimulation  replicate 3; Danio rerio; RNA Seq,GSM7885881 r1,GSM7885881,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-7-HET_S24_L002_R1_001.fastq.gz Rad21-BIO-7-HET_S24_L002_R2_001.fastq.gz,fastq fastq,4008829445.0,26560912.0,GSM7885881 r2,0:75.51 1:75.42,A:1031275075;C:966838521;G:964312635;T:1046301501;N:101713,75,75,,,1031275075,966838521,964312635,1046301501,101713,SRX22410944,SRS19443721,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.9587,0.96152,0.06791,0.06665,0.71989,0.72157,0.45962,0.46712,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28836,SRR26711854,SRX22410943,SRS19443722,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  Wnt stimulation  replicate 3,GSM7885880,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  Wnt stimulation  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885880,GSM7885880: rad21 homozygous tailbud  Wnt stimulation  replicate 3; Danio rerio; RNA Seq,GSM7885880 r1,GSM7885880,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-3-MUT_S23_L001_R1_001.fastq.gz Rad21-BIO-3-MUT_S23_L001_R2_001.fastq.gz,fastq fastq,5599192259.0,37097144.0,GSM7885880 r1,0:75.51 1:75.43,A:1432393511;C:1358888032;G:1349825352;T:1457936919;N:148445,75,75,,,1432393511,1358888032,1349825352,1457936919,148445,SRX22410943,SRS19443722,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96008,0.96296,0.0752,0.07458,0.71518,0.71595,0.45869,0.45262,76,74,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28837,SRR26711855,SRX22410943,SRS19443722,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  Wnt stimulation  replicate 3,GSM7885880,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  Wnt stimulation  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885880,GSM7885880: rad21 homozygous tailbud  Wnt stimulation  replicate 3; Danio rerio; RNA Seq,GSM7885880 r1,GSM7885880,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-3-MUT_S23_L002_R1_001.fastq.gz Rad21-BIO-3-MUT_S23_L002_R2_001.fastq.gz,fastq fastq,5635998309.0,37340801.0,GSM7885880 r2,0:75.51 1:75.43,A:1442157325;C:1367898781;G:1358570964;T:1467225614;N:145625,75,75,,,1442157325,1367898781,1358570964,1467225614,145625,SRX22410943,SRS19443722,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95976,0.96205,0.07516,0.07494,0.71415,0.71498,0.4588,0.45974,75,74,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28838,SRR26711856,SRX22410942,SRS19443720,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  no treatment  replicate 3,GSM7885879,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  no treatment  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant,GSM7885879,GSM7885879: rad21 heterozugous tailbud  no treatment  replicate 3; Danio rerio; RNA Seq,GSM7885879 r1,GSM7885879,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-7-HET_S22_L001_R1_001.fastq.gz Rad21-7-HET_S22_L001_R2_001.fastq.gz,fastq fastq,3991372523.0,26445612.0,GSM7885879 r1,0:75.50 1:75.43,A:1041422592;C:951170399;G:942539955;T:1056130915;N:108662,75,75,,,1041422592,951170399,942539955,1056130915,108662,SRX22410942,SRS19443720,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.956,0.9592,0.07986,0.07892,0.71336,0.71407,0.45912,0.45547,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28839,SRR26711857,SRX22410942,SRS19443720,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  no treatment  replicate 3,GSM7885879,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  no treatment  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant,GSM7885879,GSM7885879: rad21 heterozugous tailbud  no treatment  replicate 3; Danio rerio; RNA Seq,GSM7885879 r1,GSM7885879,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-7-HET_S22_L002_R1_001.fastq.gz Rad21-7-HET_S22_L002_R2_001.fastq.gz,fastq fastq,4014736816.0,26600423.0,GSM7885879 r2,0:75.50 1:75.43,A:1047767788;C:956861322;G:947979944;T:1062023242;N:104520,75,75,,,1047767788,956861322,947979944,1062023242,104520,SRX22410942,SRS19443720,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95647,0.9597,0.07844,0.07753,0.71342,0.71449,0.45886,0.45627,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28840,SRR26711858,SRX22410941,SRS19443719,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  no treatment  replicate 3,GSM7885878,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  no treatment  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant,GSM7885878,GSM7885878: rad21 homozygous tailbud  no treatment  replicate 3; Danio rerio; RNA Seq,GSM7885878 r1,GSM7885878,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-3-MUT_S21_L001_R1_001.fastq.gz Rad21-3-MUT_S21_L001_R2_001.fastq.gz,fastq fastq,4087719740.0,27096477.0,GSM7885878 r1,0:75.47 1:75.39,A:1036209125;C:1001425527;G:987804368;T:1062147338;N:133382,75,75,,,1036209125,1001425527,987804368,1062147338,133382,SRX22410941,SRS19443719,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95988,0.9638,0.06968,0.06927,0.71407,0.7136,0.454,0.45623,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28841,SRR26711859,SRX22410941,SRS19443719,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  no treatment  replicate 3,GSM7885878,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  no treatment  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant,GSM7885878,GSM7885878: rad21 homozygous tailbud  no treatment  replicate 3; Danio rerio; RNA Seq,GSM7885878 r1,GSM7885878,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-3-MUT_S21_L002_R1_001.fastq.gz Rad21-3-MUT_S21_L002_R2_001.fastq.gz,fastq fastq,4118276880.0,27299338.0,GSM7885878 r2,0:75.47 1:75.38,A:1044090882;C:1009018215;G:995236418;T:1069786789;N:144576,75,75,,,1044090882,1009018215,995236418,1069786789,144576,SRX22410941,SRS19443719,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96038,0.96408,0.06924,0.06885,0.71405,0.71346,0.46106,0.46176,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28842,SRR26711860,SRX22410940,SRS19443718,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  Wnt stimulation  replicate 3,GSM7885877,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,stag2b tailbud  Wnt stimulation  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation,GSM7885877,GSM7885877: stag2b tailbud  Wnt stimulation  replicate 3; Danio rerio; RNA Seq,GSM7885877 r1,GSM7885877,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-BIO-3_S20_L001_R2_001.fastq.gz S2B-BIO-3_S20_L001_R1_001.fastq.gz,fastq fastq,6393544263.0,42359569.0,GSM7885877 r1,0:75.52 1:75.42,A:1613857834;C:1576676813;G:1555975373;T:1646885701;N:148542,75,75,,,1613857834,1576676813,1555975373,1646885701,148542,SRX22410940,SRS19443718,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96254,0.96412,0.05789,0.05657,0.71928,0.71952,0.45598,0.4571,76,74,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28843,SRR26711861,SRX22410940,SRS19443718,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  Wnt stimulation  replicate 3,GSM7885877,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,stag2b tailbud  Wnt stimulation  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation,GSM7885877,GSM7885877: stag2b tailbud  Wnt stimulation  replicate 3; Danio rerio; RNA Seq,GSM7885877 r1,GSM7885877,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-BIO-3_S20_L002_R1_001.fastq.gz S2B-BIO-3_S20_L002_R2_001.fastq.gz,fastq fastq,6434553541.0,42631351.0,GSM7885877 r2,0:75.52 1:75.42,A:1624553501;C:1586927728;G:1565855680;T:1657071521;N:145111,75,75,,,1624553501,1586927728,1565855680,1657071521,145111,SRX22410940,SRS19443718,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96161,0.96439,0.05708,0.057,0.71877,0.71885,0.45079,0.45162,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28844,SRR26711862,SRX22410939,SRS19443717,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  no treatment  replicate 3,GSM7885876,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing,stag2b tailbud  no treatment  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant,GSM7885876,GSM7885876: stag2b tailbud  no treatment  replicate 3; Danio rerio; RNA Seq,GSM7885876 r1,GSM7885876,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-3_S19_L001_R2_001.fastq.gz S2B-3_S19_L001_R1_001.fastq.gz,fastq fastq,5538483383.0,36711860.0,GSM7885876 r1,0:75.47 1:75.39,A:1435032372;C:1328594066;G:1316913430;T:1457777034;N:166481,75,75,,,1435032372,1328594066,1316913430,1457777034,166481,SRX22410939,SRS19443717,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95388,0.95759,0.06115,0.05971,0.72494,0.72437,0.45251,0.45094,75,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28845,SRR26711863,SRX22410939,SRS19443717,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  no treatment  replicate 3,GSM7885876,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing,stag2b tailbud  no treatment  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant,GSM7885876,GSM7885876: stag2b tailbud  no treatment  replicate 3; Danio rerio; RNA Seq,GSM7885876 r1,GSM7885876,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-3_S19_L002_R2_001.fastq.gz S2B-3_S19_L002_R1_001.fastq.gz,fastq fastq,5571956623.0,36933840.0,GSM7885876 r2,0:75.47 1:75.39,A:1444099757;C:1336600251;G:1324816524;T:1466267099;N:172992,75,75,,,1444099757,1336600251,1324816524,1466267099,172992,SRX22410939,SRS19443717,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95377,0.95715,0.06134,0.06056,0.72342,0.72399,0.45371,0.45229,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28846,SRR26711864,SRX22410938,SRS19443716,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  Wnt stimulation  replicate 3,GSM7885875,,source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,Wild type tailbud  Wnt stimulation  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation,GSM7885875,GSM7885875: Wild type tailbud  Wnt stimulation  replicate 3; Danio rerio; RNA Seq,GSM7885875 r1,GSM7885875,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT-BIO-3_S18_L001_R2_001.fastq.gz WT-BIO-3_S18_L001_R1_001.fastq.gz,fastq fastq,2907588427.0,19272780.0,GSM7885875 r1,0:75.47 1:75.39,A:744742520;C:704673544;G:696135407;T:761933560;N:103396,75,75,,,744742520,704673544,696135407,761933560,103396,SRX22410938,SRS19443716,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95667,0.96068,0.06758,0.06662,0.71654,0.71695,0.46152,0.46391,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28847,SRR26711865,SRX22410938,SRS19443716,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  Wnt stimulation  replicate 3,GSM7885875,,source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,Wild type tailbud  Wnt stimulation  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation,GSM7885875,GSM7885875: Wild type tailbud  Wnt stimulation  replicate 3; Danio rerio; RNA Seq,GSM7885875 r1,GSM7885875,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT-BIO-3_S18_L002_R2_001.fastq.gz WT-BIO-3_S18_L002_R1_001.fastq.gz,fastq fastq,2928304522.0,19409983.0,GSM7885875 r2,0:75.47 1:75.39,A:750212329;C:709699732;G:701107247;T:767185941;N:99273,75,75,,,750212329,709699732,701107247,767185941,99273,SRX22410938,SRS19443716,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95734,0.96043,0.06712,0.06582,0.71764,0.71829,0.46986,0.46257,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28848,SRR26711866,SRX22410937,SRS19443715,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  no treatment  replicate 3,GSM7885874,,source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing,Wild type tailbud  no treatment  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type,GSM7885874,GSM7885874: Wild type tailbud  no treatment  replicate 3; Danio rerio; RNA Seq,GSM7885874 r1,GSM7885874,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT3_S17_L001_R2_001.fastq.gz WT3_S17_L001_R1_001.fastq.gz,fastq fastq,6706792771.0,44471190.0,GSM7885874 r1,0:75.45 1:75.37,A:1721256764;C:1618398945;G:1602221748;T:1764649478;N:265836,75,75,,,1721256764,1618398945,1602221748,1764649478,265836,SRX22410937,SRS19443715,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95476,0.95901,0.0654,0.06441,0.71821,0.71764,0.46826,0.46883,75,73,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28849,SRR26711867,SRX22410937,SRS19443715,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  no treatment  replicate 3,GSM7885874,,source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing,Wild type tailbud  no treatment  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type,GSM7885874,GSM7885874: Wild type tailbud  no treatment  replicate 3; Danio rerio; RNA Seq,GSM7885874 r1,GSM7885874,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT3_S17_L002_R1_001.fastq.gz WT3_S17_L002_R2_001.fastq.gz,fastq fastq,6751557772.0,44768192.0,GSM7885874 r2,0:75.45 1:75.37,A:1732864650;C:1629248349;G:1613082990;T:1776088109;N:273674,75,75,,,1732864650,1629248349,1613082990,1776088109,273674,SRX22410937,SRS19443715,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95584,0.95991,0.0649,0.0638,0.71819,0.71855,0.47015,0.46826,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28850,SRR26711868,SRX22410936,SRS19443714,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  Wnt stimulation  replicate 2,GSM7885873,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  Wnt stimulation  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885873,GSM7885873: rad21 heterozugous tailbud  Wnt stimulation  replicate 2; Danio rerio; RNA Seq,GSM7885873 r1,GSM7885873,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-6-HET_S16_L001_R1_001.fastq.gz Rad21-BIO-6-HET_S16_L001_R2_001.fastq.gz,fastq fastq,10402910048.0,68936909.0,GSM7885873 r1,0:75.49 1:75.41,A:2678222257;C:2507951720;G:2508878864;T:2707580436;N:276771,75,75,,,2678222257,2507951720,2508878864,2707580436,276771,SRX22410936,SRS19443714,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95996,0.96303,0.07074,0.07121,0.7176,0.71977,0.46271,0.46279,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28851,SRR26711869,SRX22410936,SRS19443714,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  Wnt stimulation  replicate 2,GSM7885873,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  Wnt stimulation  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885873,GSM7885873: rad21 heterozugous tailbud  Wnt stimulation  replicate 2; Danio rerio; RNA Seq,GSM7885873 r1,GSM7885873,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-6-HET_S16_L002_R1_001.fastq.gz Rad21-BIO-6-HET_S16_L002_R2_001.fastq.gz,fastq fastq,10457419135.0,69298126.0,GSM7885873 r2,0:75.49 1:75.41,A:2693018275;C:2521215208;G:2521858256;T:2721040335;N:287061,75,75,,,2693018275,2521215208,2521858256,2721040335,287061,SRX22410936,SRS19443714,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95978,0.962,0.07287,0.07218,0.71928,0.72015,0.4627,0.46327,76,74,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28852,SRR26711870,SRX22410935,SRS19443713,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  Wnt stimulation  replicate 2,GSM7885872,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  Wnt stimulation  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885872,GSM7885872: rad21 homozygous tailbud  Wnt stimulation  replicate 2; Danio rerio; RNA Seq,GSM7885872 r1,GSM7885872,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-2-MUT_S15_L001_R2_001.fastq.gz Rad21-BIO-2-MUT_S15_L001_R1_001.fastq.gz,fastq fastq,7186685076.0,47626097.0,GSM7885872 r1,0:75.50 1:75.40,A:1840710532;C:1745543326;G:1746892421;T:1853340863;N:197934,75,75,,,1840710532,1745543326,1746892421,1853340863,197934,SRX22410935,SRS19443713,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96231,0.96418,0.06946,0.06881,0.71756,0.71873,0.46166,0.45998,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28853,SRR26711871,SRX22410935,SRS19443713,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  Wnt stimulation  replicate 2,GSM7885872,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  Wnt stimulation  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885872,GSM7885872: rad21 homozygous tailbud  Wnt stimulation  replicate 2; Danio rerio; RNA Seq,GSM7885872 r1,GSM7885872,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-2-MUT_S15_L002_R2_001.fastq.gz Rad21-BIO-2-MUT_S15_L002_R1_001.fastq.gz,fastq fastq,7224888168.0,47879502.0,GSM7885872 r2,0:75.50 1:75.40,A:1851188490;C:1754962659;G:1755894085;T:1862643357;N:199577,75,75,,,1851188490,1754962659,1755894085,1862643357,199577,SRX22410935,SRS19443713,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96174,0.96335,0.06858,0.06794,0.71624,0.71752,0.46477,0.46238,74,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28854,SRR26711872,SRX22410934,SRS19443712,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  no treatment  replicate 2,GSM7885871,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  no treatment  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant,GSM7885871,GSM7885871: rad21 heterozugous tailbud  no treatment  replicate 2; Danio rerio; RNA Seq,GSM7885871 r1,GSM7885871,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-6-HET_S14_L001_R2_001.fastq.gz Rad21-6-HET_S14_L001_R1_001.fastq.gz,fastq fastq,5920802946.0,39225537.0,GSM7885871 r1,0:75.52 1:75.42,A:1518148809;C:1443498311;G:1449929695;T:1509064332;N:161799,75,75,,,1518148809,1443498311,1449929695,1509064332,161799,SRX22410934,SRS19443712,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96404,0.96544,0.06392,0.06339,0.71825,0.71956,0.45911,0.44993,75,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28855,SRR26711873,SRX22410934,SRS19443712,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  no treatment  replicate 2,GSM7885871,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  no treatment  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant,GSM7885871,GSM7885871: rad21 heterozugous tailbud  no treatment  replicate 2; Danio rerio; RNA Seq,GSM7885871 r1,GSM7885871,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-6-HET_S14_L002_R1_001.fastq.gz Rad21-6-HET_S14_L002_R2_001.fastq.gz,fastq fastq,5948197274.0,39406919.0,GSM7885871 r2,0:75.52 1:75.42,A:1525770407;C:1450296537;G:1456334492;T:1515638367;N:157471,75,75,,,1525770407,1450296537,1456334492,1515638367,157471,SRX22410934,SRS19443712,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.9635,0.96517,0.06272,0.06248,0.71804,0.72202,0.45512,0.45879,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28856,SRR26711874,SRX22410933,SRS19443711,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  no treatment  replicate 2,GSM7885870,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  no treatment  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant,GSM7885870,GSM7885870: rad21 homozygous tailbud  no treatment  replicate 2; Danio rerio; RNA Seq,GSM7885870 r1,GSM7885870,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-9-MUT_S13_L001_R2_001.fastq.gz Rad21-9-MUT_S13_L001_R1_001.fastq.gz,fastq fastq,4731957733.0,31354997.0,GSM7885870 r1,0:75.51 1:75.41,A:1201221275;C:1160116117;G:1163056871;T:1207419408;N:144062,75,75,,,1201221275,1160116117,1163056871,1207419408,144062,SRX22410933,SRS19443711,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96425,0.96472,0.06588,0.06468,0.71687,0.71942,0.4434,0.44236,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28857,SRR26711875,SRX22410933,SRS19443711,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  no treatment  replicate 2,GSM7885870,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  no treatment  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant,GSM7885870,GSM7885870: rad21 homozygous tailbud  no treatment  replicate 2; Danio rerio; RNA Seq,GSM7885870 r1,GSM7885870,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-9-MUT_S13_L002_R1_001.fastq.gz Rad21-9-MUT_S13_L002_R2_001.fastq.gz,fastq fastq,4757933550.0,31527251.0,GSM7885870 r2,0:75.51 1:75.41,A:1208392417;C:1166483269;G:1169184243;T:1213729419;N:144202,75,75,,,1208392417,1166483269,1169184243,1213729419,144202,SRX22410933,SRS19443711,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96375,0.96493,0.06559,0.06422,0.71774,0.71922,0.44693,0.43358,76,74,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28858,SRR26711876,SRX22410932,SRS19443710,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  Wnt stimulation  replicate 2,GSM7885869,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,stag2b tailbud  Wnt stimulation  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation,GSM7885869,GSM7885869: stag2b tailbud  Wnt stimulation  replicate 2; Danio rerio; RNA Seq,GSM7885869 r1,GSM7885869,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-BIO-2_S12_L001_R1_001.fastq.gz S2B-BIO-2_S12_L001_R2_001.fastq.gz,fastq fastq,3434334163.0,22753985.0,GSM7885869 r1,0:75.51 1:75.42,A:874466456;C:839309146;G:839975055;T:880508590;N:74916,75,75,,,874466456,839309146,839975055,880508590,74916,SRX22410932,SRS19443710,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96096,0.96302,0.06063,0.06064,0.71676,0.7177,0.45781,0.45685,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28859,SRR26711877,SRX22410932,SRS19443710,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  Wnt stimulation  replicate 2,GSM7885869,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,stag2b tailbud  Wnt stimulation  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation,GSM7885869,GSM7885869: stag2b tailbud  Wnt stimulation  replicate 2; Danio rerio; RNA Seq,GSM7885869 r1,GSM7885869,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-BIO-2_S12_L002_R1_001.fastq.gz S2B-BIO-2_S12_L002_R2_001.fastq.gz,fastq fastq,3455106879.0,22891438.0,GSM7885869 r2,0:75.52 1:75.42,A:880118959;C:844367467;G:844856793;T:885694827;N:68833,75,75,,,880118959,844367467,844856793,885694827,68833,SRX22410932,SRS19443710,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96044,0.96247,0.06148,0.06124,0.71892,0.72019,0.45384,0.45979,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28860,SRR26711878,SRX22410931,SRS19443708,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  no treatment  replicate 2,GSM7885868,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing,stag2b tailbud  no treatment  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant,GSM7885868,GSM7885868: stag2b tailbud  no treatment  replicate 2; Danio rerio; RNA Seq,GSM7885868 r1,GSM7885868,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-2_S11_L001_R1_001.fastq.gz S2B-2_S11_L001_R2_001.fastq.gz,fastq fastq,3538294337.0,23437308.0,GSM7885868 r1,0:75.53 1:75.44,A:911440182;C:854797688;G:851200714;T:920789817;N:65936,75,75,,,911440182,854797688,851200714,920789817,65936,SRX22410931,SRS19443708,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95621,0.95881,0.06034,0.05969,0.71816,0.71892,0.45142,0.45093,75,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28861,SRR26711879,SRX22410931,SRS19443708,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  no treatment  replicate 2,GSM7885868,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing,stag2b tailbud  no treatment  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant,GSM7885868,GSM7885868: stag2b tailbud  no treatment  replicate 2; Danio rerio; RNA Seq,GSM7885868 r1,GSM7885868,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-2_S11_L002_R1_001.fastq.gz S2B-2_S11_L002_R2_001.fastq.gz,fastq fastq,3556484158.0,23557941.0,GSM7885868 r2,0:75.53 1:75.44,A:916293958;C:859339499;G:855534732;T:925247442;N:68527,75,75,,,916293958,859339499,855534732,925247442,68527,SRX22410931,SRS19443708,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95449,0.95714,0.05993,0.05895,0.7207,0.72174,0.44213,0.44014,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28862,SRR26711880,SRX22410930,SRS19443709,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  Wnt stimulation  replicate 2,GSM7885867,,source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,Wild type tailbud  Wnt stimulation  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation,GSM7885867,GSM7885867: Wild type tailbud  Wnt stimulation  replicate 2; Danio rerio; RNA Seq,GSM7885867 r1,GSM7885867,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT-BIO-2_S10_L001_R1_001.fastq.gz WT-BIO-2_S10_L001_R2_001.fastq.gz,fastq fastq,4962467069.0,32885292.0,GSM7885867 r1,0:75.49 1:75.41,A:1261895016;C:1212881283;G:1199367390;T:1288195310;N:128070,75,75,,,1261895016,1212881283,1199367390,1288195310,128070,SRX22410930,SRS19443709,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96086,0.96361,0.06058,0.05969,0.71679,0.71614,0.46741,0.47167,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28863,SRR26711881,SRX22410930,SRS19443709,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  Wnt stimulation  replicate 2,GSM7885867,,source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,Wild type tailbud  Wnt stimulation  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation,GSM7885867,GSM7885867: Wild type tailbud  Wnt stimulation  replicate 2; Danio rerio; RNA Seq,GSM7885867 r1,GSM7885867,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT-BIO-2_S10_L002_R1_001.fastq.gz WT-BIO-2_S10_L002_R2_001.fastq.gz,fastq fastq,4987807658.0,33053054.0,GSM7885867 r2,0:75.50 1:75.41,A:1268585681;C:1219140011;G:1205507373;T:1294443086;N:131507,75,75,,,1268585681,1219140011,1205507373,1294443086,131507,SRX22410930,SRS19443709,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96019,0.96278,0.0598,0.05932,0.71837,0.71942,0.46581,0.46052,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system