{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Adult\" and tissue_curation_coarse = \"Surface Structure\"", "rows": [[282, "DRR179616", "DRX170142", "DRS185505", "DRP007318", "PRJDB8340", "Gene expression analysis of zebrafish fin melanophores and xanthophores.", "DRP007318", "Other", "Pigment cells  melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore  and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.", null, null, "Biological replicate 2", "Fin xanthophore 03", "SAMD00172019", null, "sample name:Zebrafish pigment cell 06|cell type:Xanthophore|collection date:2015 11 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing of SAMD00172019", "DRX170142", "Zebrafish fin xanthophore 01", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>232</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>", "DRP007318", "Ion Torrent PGM sequencing of SAMD00172019", null, null, null, 376558775.0, 1624500.0, "DRR179616", "0:231.80", "A:107837072;C:79508449;G:79372899;T:109840355;N:0", 231, null, null, null, 107837072, 79508449, 79372899, 109840355, 0, "DRX170142", "DRS185505", "DRA008445", "OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University", "Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University", 1, 0.86944, null, 0.10951, null, 0.90425, null, 0.59385, null, 311, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "Japan", "2021-05-21", "Adult", "Adult", "Fin", "Surface Structure"], [283, "DRR179615", "DRX170141", "DRS185504", "DRP007318", "PRJDB8340", "Gene expression analysis of zebrafish fin melanophores and xanthophores.", "DRP007318", "Other", "Pigment cells  melanophores and xanthophores were collected from zebrafish fin. 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The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.", null, null, "Biological replicate 1", "Fin melanophore 02", "SAMD00172015", null, "sample name:Zebrafish pigment cell 02|cell type:Melanophore|collection date:2015 05 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing of SAMD00172015", "DRX170138", "Zebrafish fin melanophore 02", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>216</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>", "DRP007318", "Ion Torrent PGM sequencing of SAMD00172015", null, null, null, 538412675.0, 2168231.0, "DRR179612", "0:248.32", "A:147128403;C:121854818;G:121564109;T:147865345;N:0", 248, null, null, null, 147128403, 121854818, 121564109, 147865345, 0, "DRX170138", "DRS185501", "DRA008445", "OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University", "Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University", 1, 0.89106, null, 0.07081, null, 0.89286, null, 0.5935, null, 283, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "Japan", "2021-05-21", "Adult", "Adult", "Fin", "Surface Structure"], [287, "DRR179611", "DRX170137", "DRS185500", "DRP007318", "PRJDB8340", "Gene expression analysis of zebrafish fin melanophores and xanthophores.", "DRP007318", "Other", "Pigment cells  melanophores and xanthophores were collected from zebrafish fin. 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The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.", null, null, "Biological replicate 1", "Fin melanophore 01", "SAMD00172014", null, "sample name:Zebrafish pigment cell 01|cell type:Melanophore|collection date:2015 05 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing of SAMD00172014", "DRX170137", "Zebrafish fin melanophore 01", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>215</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>", "DRP007318", "Ion Torrent PGM sequencing of SAMD00172014", null, null, null, 282446840.0, 1311431.0, "DRR179611", "0:215.37", 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from RIKEN Wild type zebrafish Adult C", "SAMD00222585", null, "sample name:Adult C", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00222585", "DRX214839", "Adult C", "1", "Illumina TruSeq Stranded mRNA Library Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008458", "Illumina NovaSeq 6000 paired end sequencing of SAMD00222585", null, null, null, 11727505800.0, 58637529.0, "DRR224554", "0:100 1:100", "A:3137648588;C:2705013210;G:3191753451;T:2692963496;N:127055", 100, 100, null, 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To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25", null, null, "Mau tVBU1/tVBU1 skin transcriptome", "SAMEA3880686", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 9", "vbu13", "1", "Illumina TruSeq RNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP014370", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16", "vbu13_GCCAAT_L008_R1_001.fastq.gz", "fastq", 2376143675.0, 23526175.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 9", "0:101", "A:655940769;C:534990399;G:527934646;T:655773043;N:1504818", 101, null, null, null, 655940769, 534990399, 527934646, 655773043, 1504818, "ERX1365625", "ERS1067820", "ERA567249", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 1, 0.95443, null, 0.10666, null, 0.73176, null, 0.50978, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [3760, "ERR1294278", "ERX1365624", "ERS1067820", "ERP014370", "PRJEB12848", "Danio rerio Mau mutants skin Transcriptome", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265", "Other", "Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25", null, null, "Mau tVBU1/tVBU1 skin transcriptome", "SAMEA3880686", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 8", "vbu12", "1", "Illumina TruSeq RNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP014370", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16", "vbu12_GTGAAA_L008_R1_001.fastq.gz", "fastq", 1449181835.0, 14348335.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 8", "0:101", "A:399518584;C:327615685;G:323868050;T:397240465;N:939051", 101, null, null, null, 399518584, 327615685, 323868050, 397240465, 939051, "ERX1365624", "ERS1067820", "ERA567249", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 1, 0.95893, null, 0.09315, null, 0.73464, null, 0.48744, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [3761, "ERR1294277", "ERX1365623", "ERS1067820", "ERP014370", "PRJEB12848", "Danio rerio Mau mutants skin Transcriptome", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265", "Other", "Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25", null, null, "Mau tVBU1/tVBU1 skin transcriptome", "SAMEA3880686", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 7", "vbu11", "1", "Illumina TruSeq RNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP014370", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16", "vbu11_GTCCGC_L008_R1_001.fastq.gz", "fastq", 1455235169.0, 14408269.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 7", "0:101", "A:392100064;C:337980617;G:331091626;T:393178582;N:884280", 101, null, null, null, 392100064, 337980617, 331091626, 393178582, 884280, "ERX1365623", "ERS1067820", "ERA567249", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 1, 0.95485, null, 0.08016, null, 0.72845, null, 0.47549, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [3762, "ERR1294276", "ERX1365622", "ERS1067819", "ERP014370", "PRJEB12848", "Danio rerio Mau mutants skin Transcriptome", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265", "Other", "Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25", null, null, "Mau tVE1/tVE1 skin transcriptome", "SAMEA3880685", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 6", "ve13", "1", "Illumina TruSeq RNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP014370", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16", "ve13_CCGTCC_L008_R1_001.fastq.gz", "fastq", 1029294030.0, 10191030.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 6", "0:101", "A:284612731;C:231451012;G:228443320;T:284135536;N:651431", 101, null, null, null, 284612731, 231451012, 228443320, 284135536, 651431, "ERX1365622", "ERS1067819", "ERA567249", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 1, 0.93287, null, 0.10726, null, 0.72585, null, 0.4913, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [3763, "ERR1294275", "ERX1365621", "ERS1067819", "ERP014370", "PRJEB12848", "Danio rerio Mau mutants skin Transcriptome", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265", "Other", "Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25", null, null, "Mau tVE1/tVE1 skin transcriptome", "SAMEA3880685", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 5", "ve12", "1", "Illumina TruSeq RNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP014370", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16", "ve12_ATGTCA_L008_R1_001.fastq.gz", "fastq", 1446322222.0, 14320022.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 5", "0:101", "A:400821160;C:324210104;G:320286425;T:400078485;N:926048", 101, null, null, null, 400821160, 324210104, 320286425, 400078485, 926048, "ERX1365621", "ERS1067819", "ERA567249", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 1, 0.92778, null, 0.09489, null, 0.73093, null, 0.48493, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [3764, "ERR1294274", "ERX1365620", "ERS1067819", "ERP014370", "PRJEB12848", "Danio rerio Mau mutants skin Transcriptome", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265", "Other", "Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25", null, null, "Mau tVE1/tVE1 skin transcriptome", "SAMEA3880685", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 4", "ve11", "1", "Illumina TruSeq RNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP014370", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16", "ve11_AGTTCC_L008_R1_001.fastq.gz", "fastq", 2117238861.0, 20962761.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 4", "0:101", "A:591654664;C:469803769;G:462550117;T:591863795;N:1366516", 101, null, null, null, 591654664, 469803769, 462550117, 591863795, 1366516, "ERX1365620", "ERS1067819", "ERA567249", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 1, 0.93146, null, 0.09666, null, 0.73501, null, 0.48749, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [3765, "ERR1294273", "ERX1365619", "ERS1067818", "ERP014370", "PRJEB12848", "Danio rerio Mau mutants skin Transcriptome", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265", "Other", "Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25", null, null, "WT skin transcriptome", "SAMEA3880684", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 3", "wt3", "1", "Illumina TruSeq RNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP014370", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16", "wt3_AGTCAA_L008_R1_001.fastq.gz", "fastq", 2631687411.0, 26056311.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 3", "0:101", "A:734843629;C:584316000;G:577487406;T:733356850;N:1683526", 101, null, null, null, 734843629, 584316000, 577487406, 733356850, 1683526, "ERX1365619", "ERS1067818", "ERA567249", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 1, 0.95114, null, 0.1036, null, 0.72474, null, 0.48261, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [3766, "ERR1294272", "ERX1365618", "ERS1067818", "ERP014370", "PRJEB12848", "Danio rerio Mau mutants skin Transcriptome", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265", "Other", "Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. 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To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25", null, null, "WT skin transcriptome", "SAMEA3880684", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:668 1", "wt1", "1", "Illumina TruSeq RNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP014370", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16", "wt1_CAGATC_L008_R1_001.fastq.gz", "fastq", 1701561241.0, 16847141.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:668 1", "0:101", "A:505358711;C:348893979;G:343445186;T:502880170;N:983195", 101, null, null, null, 505358711, 348893979, 343445186, 502880170, 983195, "ERX1365617", "ERS1067818", "ERA567249", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 1, 0.94565, null, 0.13032, null, 0.73669, null, 0.50473, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [9170, "ERR216332", "ERX190997", "ERS094086", "ERP001234", "PRJEB2894", "ZF adult transcriptome", "ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125", "Transcriptome Analysis", "Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.", null, null, null, null, "SAMEA1689285", "SC", "ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:37Z|External Id:SAMEA1689285|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:37Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:29Z 1355130|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:29Z 1355130|scientific name:Danio rerio|strain:SAT", null, null, null, null, null, null, null, null, "1", "SC EXP 7896 6#6", "4927108", "Illumina sequencing of library 4927108  constructed from sample accession ERS094086 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence GCCAATGT.", "Illumina cDNA protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP001234", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16", "7896_6#6.bam", "bam", 3849223200.0, 25661488.0, "SC RUN 7896 6#6", "0:75 1:75", "A:1052343872;C:867977827;G:867966925;T:1060514703;N:419873", 75, 75, null, null, 1052343872, 867977827, 867966925, 1060514703, 419873, "ERX190997", "ERS094086", "ERA182034", "SC", "Wellcome Sanger Institute", 2, 0.94843, 0.9504, 0.09374, 0.09366, 0.71421, 0.71916, 0.5306, 0.52809, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2013-01-07", "Adult", "Adult", "Trunk", "Surface Structure"], [9171, "ERR216331", "ERX190996", "ERS094085", "ERP001234", "PRJEB2894", "ZF adult transcriptome", "ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125", "Transcriptome Analysis", "Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.", null, null, null, null, "SAMEA1689286", "SC", "ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:15Z|External Id:SAMEA1689286|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:15Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:28Z 1355129|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:28Z 1355129|scientific name:Danio rerio|strain:SAT", null, null, null, null, null, null, null, null, "1", "SC EXP 7896 6#5", "4927107", "Illumina sequencing of library 4927107  constructed from sample accession ERS094085 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence ACAGTGGT.", "Illumina cDNA protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP001234", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16", "7896_6#5.bam", "bam", 5957027700.0, 39713518.0, "SC RUN 7896 6#5", "0:75 1:75", "A:1634176455;C:1344899134;G:1345048404;T:1632256963;N:646744", 75, 75, null, null, 1634176455, 1344899134, 1345048404, 1632256963, 646744, "ERX190996", "ERS094085", "ERA182034", "SC", "Wellcome Sanger Institute", 2, 0.94169, 0.94387, 0.09489, 0.09587, 0.69406, 0.69869, 0.51459, 0.51918, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2013-01-07", "Adult", "Adult", "Trunk", "Surface Structure"], [9172, "ERR216330", "ERX190995", "ERS094084", "ERP001234", "PRJEB2894", "ZF adult transcriptome", "ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125", "Transcriptome Analysis", "Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.", null, null, null, null, "SAMEA1689283", "SC", "ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:37Z|External Id:SAMEA1689283|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:37Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:28Z 1355128|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:28Z 1355128|scientific name:Danio rerio|strain:SAT", null, null, null, null, null, null, null, null, "1", "SC EXP 7896 6#4", "4927106", "Illumina sequencing of library 4927106  constructed from sample accession ERS094084 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence TGACCACT.", "Illumina cDNA protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP001234", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16", "7896_6#4.bam", "bam", 4130918700.0, 27539458.0, "SC RUN 7896 6#4", "0:75 1:75", "A:1129107864;C:933544249;G:934913323;T:1132901907;N:451357", 75, 75, null, null, 1129107864, 933544249, 934913323, 1132901907, 451357, "ERX190995", "ERS094084", "ERA182034", "SC", "Wellcome Sanger Institute", 2, 0.94225, 0.94433, 0.09272, 0.09299, 0.70043, 0.70534, 0.51333, 0.52182, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2013-01-07", "Adult", "Adult", "Trunk", "Surface Structure"], [9173, "ERR216329", "ERX190994", "ERS094083", "ERP001234", "PRJEB2894", "ZF adult transcriptome", "ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125", "Transcriptome Analysis", "Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.", null, null, null, null, "SAMEA1689282", "SC", "ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:37Z|External Id:SAMEA1689282|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:37Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:27Z 1355127|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:27Z 1355127|scientific name:Danio rerio|strain:SAT", null, null, null, null, null, null, null, null, "1", "SC EXP 7896 6#3", "4927105", "Illumina sequencing of library 4927105  constructed from sample accession ERS094083 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence TTAGGCAT.", "Illumina cDNA protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP001234", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16", "7896_6#3.bam", "bam", 5102725800.0, 34018172.0, "SC RUN 7896 6#3", "0:75 1:75", "A:1400946711;C:1145033579;G:1143298888;T:1412890130;N:556492", 75, 75, null, null, 1400946711, 1145033579, 1143298888, 1412890130, 556492, "ERX190994", "ERS094083", "ERA182034", "SC", "Wellcome Sanger Institute", 2, 0.93688, 0.93952, 0.07363, 0.07321, 0.69645, 0.70161, 0.48708, 0.48926, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2013-01-07", "Adult", "Adult", "Trunk", "Surface Structure"], [9174, "ERR216328", "ERX190993", "ERS094082", "ERP001234", "PRJEB2894", "ZF adult transcriptome", "ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125", "Transcriptome Analysis", "Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.", null, null, null, null, "SAMEA1689281", "SC", "ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T10:04:12Z|ENA LAST UPDATE:2018 03 08T15:36:11Z|External Id:SAMEA1689281|INSDC center name:SC|INSDC first public:2013 01 07T10:04:12Z|INSDC last update:2018 03 08T15:36:11Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:26Z 1355126|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:26Z 1355126|scientific name:Danio rerio|strain:SAT", null, null, null, null, null, null, null, null, "1", "SC EXP 7896 6#2", "4927104", "Illumina sequencing of library 4927104  constructed from sample accession ERS094082 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence CGATGTTT.", "Illumina cDNA protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP001234", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16", "7896_6#2.bam", "bam", 4350577950.0, 29003853.0, "SC RUN 7896 6#2", "0:75 1:75", "A:1214100125;C:955724962;G:954429461;T:1225838270;N:485132", 75, 75, null, null, 1214100125, 955724962, 954429461, 1225838270, 485132, "ERX190993", "ERS094082", "ERA182034", "SC", "Wellcome Sanger Institute", 2, 0.92911, 0.93026, 0.0749, 0.07514, 0.69418, 0.69775, 0.48934, 0.49, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2013-01-07", "Adult", "Adult", "Trunk", "Surface Structure"], [9175, "ERR216327", "ERX190992", "ERS094081", "ERP001234", "PRJEB2894", "ZF adult transcriptome", "ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125", "Transcriptome Analysis", "Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.", null, null, null, null, "SAMEA1689284", "SC", "ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:37Z|External Id:SAMEA1689284|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:37Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:23Z 1355125|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:23Z 1355125|scientific name:Danio rerio|strain:SAT", null, null, null, null, null, null, null, null, "1", "SC EXP 7896 6#1", "4927103", "Illumina sequencing of library 4927103  constructed from sample accession ERS094081 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence ATCACGTT.", "Illumina cDNA protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP001234", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16", "7896_6#1.bam", "bam", 5063629350.0, 33757529.0, "SC RUN 7896 6#1", "0:75 1:75", "A:1416301768;C:1110273098;G:1105481234;T:1431015934;N:557316", 75, 75, null, null, 1416301768, 1110273098, 1105481234, 1431015934, 557316, "ERX190992", "ERS094081", "ERA182034", "SC", "Wellcome Sanger Institute", 2, 0.93508, 0.93634, 0.11212, 0.11206, 0.70009, 0.70538, 0.50126, 0.49177, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2013-01-07", "Adult", "Adult", "Trunk", "Surface Structure"], [9770, "ERR5838122", "ERX5487778", "ERS6337138", "ERP119543", "PRJEB36360", "Transcriptomic analysis of adult skin from 9 Danio species", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27", "Other", "Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.", "ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21", "PUBMED:33277491", "Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.", "Transcriptomic analysis of adult skin from 9 Danio species", "SAMEA8652584", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652584|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:05 Danio rerio adult skin 5|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:05 Danio rerio adult skin 5|sex:male|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 5", "unspecified", "1", "TruSeq stranded mRNA Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP119543", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29", "S1385Nr5.1.fastq.gz S1385Nr5.2.fastq.gz", "fastq fastq", 6912206316.0, 34306523.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 5", "0:100.74 1:100.74", "A:1853779551;C:1607929988;G:1658402611;T:1792045990;N:48176", 100, 100, null, null, 1853779551, 1607929988, 1658402611, 1792045990, 48176, "ERX5487778", "ERS6337138", "ERA4129786", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 2, 0.96095, 0.962, 0.08049, 0.07821, 0.70654, 0.70926, 0.51398, 0.51064, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2020-03-21", "Adult", "Adult", "Skin", "Surface Structure"], [9771, "ERR5838121", "ERX5487777", "ERS6337136", "ERP119543", "PRJEB36360", "Transcriptomic analysis of adult skin from 9 Danio species", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27", "Other", "Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.", "ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21", "PUBMED:33277491", "Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.", "Transcriptomic analysis of adult skin from 9 Danio species", "SAMEA8652582", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652582|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:04 Danio rerio adult skin 4|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:04 Danio rerio adult skin 4|sex:male|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 4", "unspecified", "1", "TruSeq stranded mRNA Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP119543", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29", "S1385Nr4.1.fastq.gz S1385Nr4.2.fastq.gz", "fastq fastq", 6161942050.0, 30595009.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 4", "0:100.70 1:100.70", "A:1642716052;C:1446485458;G:1490121106;T:1582576605;N:42829", 100, 100, null, null, 1642716052, 1446485458, 1490121106, 1582576605, 42829, "ERX5487777", "ERS6337136", "ERA4129786", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 2, 0.96544, 0.96564, 0.07368, 0.07303, 0.70822, 0.71092, 0.50154, 0.50781, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2020-03-21", "Adult", "Adult", "Skin", "Surface Structure"], [9772, "ERR5838120", "ERX5487776", "ERS6337133", "ERP119543", "PRJEB36360", "Transcriptomic analysis of adult skin from 9 Danio species", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27", "Other", "Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.", "ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21", "PUBMED:33277491", "Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.", "Transcriptomic analysis of adult skin from 9 Danio species", "SAMEA8652579", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652579|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:03 Danio rerio adult skin 3|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:03 Danio rerio adult skin 3|sex:female|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 3", "unspecified", "1", "TruSeq stranded mRNA Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP119543", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29", "S1385Nr3.1.fastq.gz S1385Nr3.2.fastq.gz", "fastq fastq", 7422881394.0, 36866805.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 3", "0:100.67 1:100.67", "A:1950275527;C:1768648993;G:1827362519;T:1876542858;N:51497", 100, 100, null, null, 1950275527, 1768648993, 1827362519, 1876542858, 51497, "ERX5487776", "ERS6337133", "ERA4129786", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 2, 0.97031, 0.97047, 0.04915, 0.04817, 0.71459, 0.71894, 0.51089, 0.5097, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2020-03-21", "Adult", "Adult", "Skin", "Surface Structure"], [9773, "ERR5838119", "ERX5487775", "ERS6337132", "ERP119543", "PRJEB36360", "Transcriptomic analysis of adult skin from 9 Danio species", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27", "Other", "Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.", "ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21", "PUBMED:33277491", "Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.", "Transcriptomic analysis of adult skin from 9 Danio species", "SAMEA8652578", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652578|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:02 Danio rerio adult skin 2|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:02 Danio rerio adult skin 2|sex:female|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 2", "unspecified", "1", "TruSeq stranded mRNA Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP119543", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29", "S1385Nr2.1.fastq.gz S1385Nr2.2.fastq.gz", "fastq fastq", 7006718028.0, 34786110.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 2", "0:100.71 1:100.71", "A:1847371523;C:1665346769;G:1712373266;T:1781565768;N:60702", 100, 100, null, null, 1847371523, 1665346769, 1712373266, 1781565768, 60702, "ERX5487775", "ERS6337132", "ERA4129786", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 2, 0.96136, 0.96039, 0.05872, 0.05752, 0.70325, 0.70674, 0.46717, 0.48218, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2020-03-21", "Adult", "Adult", "Skin", "Surface Structure"], [9774, "ERR5838118", "ERX5487774", "ERS6337063", "ERP119543", "PRJEB36360", "Transcriptomic analysis of adult skin from 9 Danio species", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27", "Other", "Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.", "ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21", "PUBMED:33277491", "Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.", "Transcriptomic analysis of adult skin from 9 Danio species", "SAMEA8652509", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652509|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:01 Danio rerio adult skin 1|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:01 Danio rerio adult skin 1|sex:male|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 1", "unspecified", "1", "TruSeq stranded mRNA Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP119543", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29", "S1385Nr1.1.fastq.gz S1385Nr1.2.fastq.gz", "fastq fastq", 6586457266.0, 32719900.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 1", "0:100.65 1:100.65", "A:1709547533;C:1593125315;G:1617088678;T:1666650824;N:44916", 100, 100, null, null, 1709547533, 1593125315, 1617088678, 1666650824, 44916, "ERX5487774", "ERS6337063", "ERA4129786", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 2, 0.9531, 0.95366, 0.07763, 0.07567, 0.71384, 0.71634, 0.52409, 0.52475, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2020-03-21", "Adult", "Adult", "Skin", "Surface Structure"], [9970, "ERR5056255", "ERX4862324", "ERS4959151", "ERP123551", "PRJEB39971", "RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration", "ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170", "Other", "RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.", "bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20", null, "9 days post harvest", "Zebrafish scale RNA seq total RNA", "SAMEA7198930", "University of Bristol", "ENA first public:2021 04 20|ENA last update:2020 08 20|External Id:SAMEA7198930|INSDC center alias:BRISTOL|INSDC center name:University of Bristol|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 3|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 3|sex:male|tissue type:Elasmoid scale", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 10", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP123551", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08", "ZFG-15-01_REG3_CTTGTA_L002_R1_001.fastq.gz", "fastq", 435534645.0, 8539895.0, "ena RUN BRISTOL 08 01 2021 15:14:53:483 10", "0:51 1:0", "A:104994334;C:102642310;G:101303422;T:126578362;N:16217", 51, 0, null, null, 104994334, 102642310, 101303422, 126578362, 16217, "ERX4862324", "ERS4959151", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.92322, null, 0.08481, null, 0.71997, null, 0.45351, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [9971, "ERR5056093", "ERX4862162", "ERS4959146", "ERP123551", "PRJEB39971", "RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration", "ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170", "Other", "RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.", "bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20", null, "day x", "Zebrafish scale RNA seq total RNA", "SAMEA7198925", "BRISTOL", "ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198925|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 1|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 1|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 13:16:55:212 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP123551", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08", "ZFG-15-01_ONT1_CGATGT_L002_R1_001.fastq.gz", "fastq", 613101549.0, 12021599.0, "ena RUN BRISTOL 08 01 2021 13:16:55:212 1", "0:51 1:0", "A:152016801;C:139221646;G:139332264;T:182506912;N:23926", 51, 0, null, null, 152016801, 139221646, 139332264, 182506912, 23926, "ERX4862162", "ERS4959146", "ERA3206646", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.90335, null, 0.1072, null, 0.71784, null, 0.48228, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [9972, "ERR5056077", "ERX4862146", "ERS4959146", "ERP123551", "PRJEB39971", "RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration", "ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170", "Other", "RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.", "bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20", null, "day x", "Zebrafish scale RNA seq total RNA", "SAMEA7198925", "BRISTOL", "ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198925|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 1|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 1|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 12:07:14:527 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP123551", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08", "ZFG-15-01_ONT1_CGATGT_L001_R1_001.fastq.gz", "fastq", 600285402.0, 11770302.0, "ena RUN BRISTOL 08 01 2021 12:07:14:527 1", "0:51 1:0", "A:148729943;C:136337224;G:136545524;T:178606078;N:66633", 51, 0, null, null, 148729943, 136337224, 136545524, 178606078, 66633, "ERX4862146", "ERS4959146", "ERA3206631", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.9026, null, 0.10732, null, 0.71683, null, 0.47346, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [9973, "ERR5056254", "ERX4862323", "ERS4959151", "ERP123551", "PRJEB39971", "RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration", "ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170", "Other", "RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.", "bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20", null, "9 days post harvest", "Zebrafish scale RNA seq total RNA", "SAMEA7198930", "University of Bristol", "ENA first public:2021 04 20|ENA last update:2020 08 20|External Id:SAMEA7198930|INSDC center alias:BRISTOL|INSDC center name:University of Bristol|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 3|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 3|sex:male|tissue type:Elasmoid scale", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 9", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP123551", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08", "ZFG-15-01_REG3_CTTGTA_L001_R1_001.fastq.gz", "fastq", 426117342.0, 8355242.0, "ena RUN BRISTOL 08 01 2021 15:14:53:483 9", "0:51 1:0", "A:102630499;C:100472291;G:99193964;T:123775368;N:45220", 51, 0, null, null, 102630499, 100472291, 99193964, 123775368, 45220, "ERX4862323", "ERS4959151", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.92245, null, 0.08463, null, 0.71877, null, 0.45377, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [9974, "ERR5056253", "ERX4862322", "ERS4959150", "ERP123551", "PRJEB39971", "RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration", "ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170", "Other", "RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.", "bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20", null, "9 days post harvest", "Zebrafish scale RNA seq total RNA", "SAMEA7198929", "BRISTOL", "ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198929|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 2|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 2|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 8", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP123551", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08", "ZFG-15-01_REG2_CAGATC_L002_R1_001.fastq.gz", "fastq", 434571714.0, 8521014.0, "ena RUN BRISTOL 08 01 2021 15:14:53:483 8", "0:51 1:0", "A:106135147;C:102194661;G:100594136;T:125630448;N:17322", 51, 0, null, null, 106135147, 102194661, 100594136, 125630448, 17322, "ERX4862322", "ERS4959150", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.91779, null, 0.08112, null, 0.7161, null, 0.4437, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [9975, "ERR5056252", "ERX4862321", "ERS4959150", "ERP123551", "PRJEB39971", "RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration", "ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170", "Other", "RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.", "bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20", null, "9 days post harvest", "Zebrafish scale RNA seq total RNA", "SAMEA7198929", "BRISTOL", "ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198929|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 2|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 2|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 7", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP123551", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08", "ZFG-15-01_REG2_CAGATC_L001_R1_001.fastq.gz", "fastq", 424788384.0, 8329184.0, "ena RUN BRISTOL 08 01 2021 15:14:53:483 7", "0:51 1:0", "A:103644078;C:99946940;G:98381633;T:122768121;N:47612", 51, 0, null, null, 103644078, 99946940, 98381633, 122768121, 47612, "ERX4862321", "ERS4959150", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.91867, null, 0.08097, null, 0.71388, null, 0.44882, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [9976, "ERR5056251", "ERX4862320", "ERS4959149", "ERP123551", "PRJEB39971", "RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration", "ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170", "Other", "RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.", "bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20", null, "9 days post harvest", "Zebrafish scale RNA seq total RNA", "SAMEA7198928", "BRISTOL", "ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198928|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 1|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 1|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 6", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP123551", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08", "ZFG-15-01_REG1_GCCAAT_L002_R1_001.fastq.gz", "fastq", 481725498.0, 9445598.0, "ena RUN BRISTOL 08 01 2021 15:14:53:482 6", "0:51 1:0", "A:117075718;C:111922649;G:112057835;T:140651082;N:18214", 51, 0, null, null, 117075718, 111922649, 112057835, 140651082, 18214, "ERX4862320", "ERS4959149", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.91312, null, 0.08654, null, 0.71747, null, 0.46716, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [9977, "ERR5056250", "ERX4862319", "ERS4959149", "ERP123551", "PRJEB39971", "RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration", "ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170", "Other", "RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.", "bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20", null, "9 days post harvest", "Zebrafish scale RNA seq total RNA", "SAMEA7198928", "BRISTOL", "ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198928|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 1|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 1|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 5", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP123551", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08", "ZFG-15-01_REG1_GCCAAT_L001_R1_001.fastq.gz", "fastq", 471197976.0, 9239176.0, "ena RUN BRISTOL 08 01 2021 15:14:53:482 5", "0:51 1:0", "A:114367789;C:109551764;G:109678406;T:137546387;N:53630", 51, 0, null, null, 114367789, 109551764, 109678406, 137546387, 53630, "ERX4862319", "ERS4959149", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.91412, null, 0.08674, null, 0.71632, null, 0.46601, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [9978, "ERR5056249", "ERX4862318", "ERS4959148", "ERP123551", "PRJEB39971", "RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration", "ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170", "Other", "RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.", "bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20", null, "day x", "Zebrafish scale", "SAMEA7198927", "BRISTOL", "ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198927|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 3|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 3|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 4", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP123551", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08", "ZFG-15-01_ONT3_ACAGTG_L002_R1_001.fastq.gz", "fastq", 470142531.0, 9218481.0, "ena RUN BRISTOL 08 01 2021 15:14:53:482 4", "0:51 1:0", "A:116971308;C:106056823;G:107128214;T:139968487;N:17699", 51, 0, null, null, 116971308, 106056823, 107128214, 139968487, 17699, "ERX4862318", "ERS4959148", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.90722, null, 0.1158, null, 0.72287, null, 0.46674, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [9979, "ERR5056248", "ERX4862317", "ERS4959148", "ERP123551", "PRJEB39971", "RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration", "ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170", "Other", "RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.", "bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20", null, "day x", "Zebrafish scale", "SAMEA7198927", "BRISTOL", "ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198927|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 3|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 3|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 3", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP123551", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08", "ZFG-15-01_ONT3_ACAGTG_L001_R1_001.fastq.gz", "fastq", 460312587.0, 9025737.0, "ena RUN BRISTOL 08 01 2021 15:14:53:482 3", "0:51 1:0", "A:114396758;C:103865119;G:105005018;T:136994559;N:51133", 51, 0, null, null, 114396758, 103865119, 105005018, 136994559, 51133, "ERX4862317", "ERS4959148", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.90759, null, 0.11359, null, 0.7208, null, 0.47232, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [9980, "ERR5056247", "ERX4862316", "ERS4959147", "ERP123551", "PRJEB39971", "RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration", "ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170", "Other", "RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.", "bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20", null, "day x", "Zebrafish scale RNA seq total RNA", "SAMEA7198926", "BRISTOL", "ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198926|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 2|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 2|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 2", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP123551", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08", "ZFG-15-01_ONT2_TGACCA_L002_R1_001.fastq.gz", "fastq", 502898046.0, 9860746.0, "ena RUN BRISTOL 08 01 2021 15:14:53:482 2", "0:51 1:0", "A:123893447;C:111981365;G:116049412;T:150953220;N:20602", 51, 0, null, null, 123893447, 111981365, 116049412, 150953220, 20602, "ERX4862316", "ERS4959147", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.90777, null, 0.11921, null, 0.7137, null, 0.48182, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [9981, "ERR5056246", "ERX4862315", "ERS4959147", "ERP123551", "PRJEB39971", "RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration", "ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170", "Other", "RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.", "bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20", null, "day x", "Zebrafish scale RNA seq total RNA", "SAMEA7198926", "BRISTOL", "ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198926|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 2|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 2|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP123551", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08", "ZFG-15-01_ONT2_TGACCA_L001_R1_001.fastq.gz", "fastq", 491866134.0, 9644434.0, "ena RUN BRISTOL 08 01 2021 15:14:53:482 1", "0:51 1:0", "A:121063841;C:109534722;G:113610951;T:147602721;N:53899", 51, 0, null, null, 121063841, 109534722, 113610951, 147602721, 53899, "ERX4862315", "ERS4959147", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.907, null, 0.11935, null, 0.71364, null, 0.48543, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [25297, "SRR25764099", "SRX21486772", "SRS18719072", "SRP457109", "PRJNA1009810", "Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish", "GSE241757", "Transcriptome Analysis", "Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.", null, "pubmed:38265193", null, "Adult itgb4+ basal cells", "GSM7734879", null, "tissue:epidermal cells|cell type:adult fin epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing", "Adult itgb4+ basal cells", "High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.", "epidermal cells", "Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer\u2019s protocol.", "Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 \u00b0C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.", "cell type:adult fin epidermal basal cells|genotype:Tgitgb4:mcherry", "GSM7734879", "GSM7734879: Adult itgb4+ basal cells; Danio rerio; RNA Seq", "GSM7734879 r1", "GSM7734879", "1", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP457109", null, null, "Adult_itgb4mcherry_S230_R1_001.fastq.gz Adult_itgb4mcherry_S230_R2_001.fastq.gz", "fastq fastq", 5035430000.0, 12588575.0, "GSM7734879 r1", "0:200 1:200", "A:1339392170;C:1117195164;G:1254708952;T:1323174485;N:959229", 200, 200, null, null, 1339392170, 1117195164, 1254708952, 1323174485, 959229, "SRX21486772", "SRS18719072", "SRA1700438", "Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology", "Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology", 2, 0.01543, 0.02468, 0.00098, 0.00102, 0.99318, 0.99387, 0.47878, 0.31718, 200, 200, "T", "T", "mates < 9% mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2023-08-28", "Adult", "Adult", "Skin", "Surface Structure"], [29191, "SRR27308233", "SRX22985581", "SRS19950789", "SRP479308", "PRJNA1055256", "Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish", "GSE251757", "Transcriptome Analysis", "Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development  growth  and homeostasis. However  developmental origins of osteoblasts and chondroblasts  lineage relationship  progenitor cells  and their differentiation potentials throughout animal life are not seamlessly understood. In this study  we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages  and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed  they never change their lineage identities throughout their lives  even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells  OPCs  which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin  we isolated sp7  mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs  chondrogenic mesenchymal progenitors CMPs  and osteoblasts.", null, "pubmed:38193362", null, "EGFP /sp7+  Osteoblast  rep2", "GSM7987448", null, "source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Osteoblasts|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing", "EGFP /sp7+  Osteoblast  rep2", "High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id  length  Genbank id  RNA type  gene name  product  raw count  RPKM and TPM values.", "14 dpa adult caudal fin", "Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer\u2019s protocol.", "Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 \u00b0C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.", "tissue:14 dpa adult caudal fin|cell type:Osteoblasts|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry", "GSM7987448", "GSM7987448: EGFP /sp7+  Osteoblast  rep2; Danio rerio; RNA Seq", "GSM7987448 r1", "GSM7987448", "1", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP479308", null, null, "Ob-GR2_S6_R2_001.fastq.gz Ob-GR2_S6_R1_001.fastq.gz", "fastq fastq", 6044999600.0, 15112499.0, "GSM7987448 r1", "0:200 1:200", "A:1547731745;C:1388120378;G:1581574912;T:1523597213;N:3975352", 200, 200, null, null, 1547731745, 1388120378, 1581574912, 1523597213, 3975352, "SRX22985581", "SRS19950789", "SRA1773396", "Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology", "Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology", 2, 0.36888, 0.02272, 0.01109, 0.00038, 0.86914, 0.99328, 0.46943, 0.4982, 200, 200, "B", "T", "mate2 technical by mapping diff", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2023-12-20", "Adult", "Adult", "Fin", "Surface Structure"], [29192, "SRR27308234", "SRX22985580", "SRS19950790", "SRP479308", "PRJNA1055256", "Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish", "GSE251757", "Transcriptome Analysis", "Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development  growth  and homeostasis. However  developmental origins of osteoblasts and chondroblasts  lineage relationship  progenitor cells  and their differentiation potentials throughout animal life are not seamlessly understood. In this study  we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages  and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed  they never change their lineage identities throughout their lives  even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells  OPCs  which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin  we isolated sp7  mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs  chondrogenic mesenchymal progenitors CMPs  and osteoblasts.", null, "pubmed:38193362", null, "EGFP /sp7+  Osteoblast  rep1", "GSM7987447", null, "source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Osteoblasts|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing", "EGFP /sp7+  Osteoblast  rep1", "High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id  length  Genbank id  RNA type  gene name  product  raw count  RPKM and TPM values.", "14 dpa adult caudal fin", "Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer\u2019s protocol.", "Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 \u00b0C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.", "tissue:14 dpa adult caudal fin|cell type:Osteoblasts|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry", "GSM7987447", "GSM7987447: EGFP /sp7+  Osteoblast  rep1; Danio rerio; RNA Seq", "GSM7987447 r1", "GSM7987447", "1", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP479308", null, null, "Ob-GR_S77_R1_001.fastq.gz Ob-GR_S77_R2_001.fastq.gz", "fastq fastq", 4847773600.0, 12119434.0, "GSM7987447 r1", "0:200 1:200", "A:1242312480;C:1120397684;G:1256425065;T:1226991694;N:1646677", 200, 200, null, null, 1242312480, 1120397684, 1256425065, 1226991694, 1646677, "SRX22985580", "SRS19950790", "SRA1773396", "Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology", "Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology", 2, 0.0146, 0.02559, 0.00038, 0.00052, 0.99397, 0.99405, 0.50471, 0.47146, 200, 200, "T", "T", "mates < 9% mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2023-12-20", "Adult", "Adult", "Fin", "Surface Structure"], [29193, "SRR27308235", "SRX22985579", "SRS19950788", "SRP479308", "PRJNA1055256", "Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish", "GSE251757", "Transcriptome Analysis", "Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development  growth  and homeostasis. However  developmental origins of osteoblasts and chondroblasts  lineage relationship  progenitor cells  and their differentiation potentials throughout animal life are not seamlessly understood. In this study  we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages  and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed  they never change their lineage identities throughout their lives  even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells  OPCs  which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin  we isolated sp7  mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs  chondrogenic mesenchymal progenitors CMPs  and osteoblasts.", null, "pubmed:38193362", null, "EGFP+/sp7+  OMP  rep2", "GSM7987446", null, "source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Osteogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing", "EGFP+/sp7+  OMP  rep2", "High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id  length  Genbank id  RNA type  gene name  product  raw count  RPKM and TPM values.", "14 dpa adult caudal fin", "Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer\u2019s protocol.", "Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 \u00b0C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.", "tissue:14 dpa adult caudal fin|cell type:Osteogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry", "GSM7987446", "GSM7987446: EGFP+/sp7+  OMP  rep2; Danio rerio; RNA Seq", "GSM7987446 r1", "GSM7987446", "1", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP479308", null, null, "Ob-G2_S5_R2_001.fastq.gz Ob-G2_S5_R1_001.fastq.gz", "fastq fastq", 6253558800.0, 15633897.0, "GSM7987446 r1", "0:200 1:200", "A:1638931864;C:1404420075;G:1600115132;T:1605939571;N:4152158", 200, 200, null, null, 1638931864, 1404420075, 1600115132, 1605939571, 4152158, "SRX22985579", "SRS19950788", "SRA1773396", "Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology", "Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology", 2, 0.41021, 0.02334, 0.01523, 0.00074, 0.83989, 0.99099, 0.52255, 0.52173, 200, 200, "B", "T", "mate2 technical by mapping diff", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2023-12-20", "Adult", "Adult", "Fin", "Surface Structure"], [29194, "SRR27308236", "SRX22985578", "SRS19950791", "SRP479308", "PRJNA1055256", "Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish", "GSE251757", "Transcriptome Analysis", "Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development  growth  and homeostasis. However  developmental origins of osteoblasts and chondroblasts  lineage relationship  progenitor cells  and their differentiation potentials throughout animal life are not seamlessly understood. In this study  we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages  and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed  they never change their lineage identities throughout their lives  even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells  OPCs  which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin  we isolated sp7  mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs  chondrogenic mesenchymal progenitors CMPs  and osteoblasts.", null, "pubmed:38193362", null, "EGFP+/sp7+  OMP  rep1", "GSM7987445", null, "source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Osteogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing", "EGFP+/sp7+  OMP  rep1", "High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id  length  Genbank id  RNA type  gene name  product  raw count  RPKM and TPM values.", "14 dpa adult caudal fin", "Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer\u2019s protocol.", "Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 \u00b0C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.", "tissue:14 dpa adult caudal fin|cell type:Osteogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry", "GSM7987445", "GSM7987445: EGFP+/sp7+  OMP  rep1; Danio rerio; RNA Seq", "GSM7987445 r1", "GSM7987445", "1", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP479308", null, null, "Ob-G_S28_R2_001.fastq.gz Ob-G_S28_R1_001.fastq.gz", "fastq fastq", 4832320400.0, 12080801.0, "GSM7987445 r1", "0:200 1:200", "A:1252095509;C:1107971153;G:1236349772;T:1233319775;N:2584191", 200, 200, null, null, 1252095509, 1107971153, 1236349772, 1233319775, 2584191, "SRX22985578", "SRS19950791", "SRA1773396", "Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology", "Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology", 2, 0.01133, 0.02895, 0.00033, 0.00043, 0.99439, 0.99297, 0.50298, 0.45574, 200, 200, "T", "T", "mates < 9% mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2023-12-20", "Adult", "Adult", "Fin", "Surface Structure"], [29195, "SRR27308237", "SRX22985577", "SRS19950787", "SRP479308", "PRJNA1055256", "Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish", "GSE251757", "Transcriptome Analysis", "Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development  growth  and homeostasis. However  developmental origins of osteoblasts and chondroblasts  lineage relationship  progenitor cells  and their differentiation potentials throughout animal life are not seamlessly understood. In this study  we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages  and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed  they never change their lineage identities throughout their lives  even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells  OPCs  which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin  we isolated sp7  mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs  chondrogenic mesenchymal progenitors CMPs  and osteoblasts.", null, "pubmed:38193362", null, "EGFP+/sp7   CMP  rep2", "GSM7987444", null, "source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Chondrogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing", "EGFP+/sp7   CMP  rep2", "High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id  length  Genbank id  RNA type  gene name  product  raw count  RPKM and TPM values.", "14 dpa adult caudal fin", "Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer\u2019s protocol.", "Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 \u00b0C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.", "tissue:14 dpa adult caudal fin|cell type:Chondrogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry", "GSM7987444", "GSM7987444: EGFP+/sp7   CMP  rep2; Danio rerio; RNA Seq", "GSM7987444 r1", "GSM7987444", "1", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP479308", null, null, "Mes-G2_S4_R1_001.fastq.gz Mes-G2_S4_R2_001.fastq.gz", "fastq fastq", 5812163600.0, 14530409.0, "GSM7987444 r1", "0:200 1:200", "A:1538664561;C:1291748975;G:1473028809;T:1504905134;N:3816121", 200, 200, null, null, 1538664561, 1291748975, 1473028809, 1504905134, 3816121, "SRX22985577", "SRS19950787", "SRA1773396", "Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology", "Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology", 2, 0.40138, 0.02482, 0.0176, 0.00091, 0.83918, 0.99099, 0.47875, 0.43124, 200, 200, "B", "T", "mate2 technical by mapping diff", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2023-12-20", "Adult", "Adult", "Fin", "Surface Structure"], [29196, "SRR27308238", "SRX22985576", "SRS19950786", "SRP479308", "PRJNA1055256", "Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish", "GSE251757", "Transcriptome Analysis", "Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development  growth  and homeostasis. However  developmental origins of osteoblasts and chondroblasts  lineage relationship  progenitor cells  and their differentiation potentials throughout animal life are not seamlessly understood. In this study  we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages  and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed  they never change their lineage identities throughout their lives  even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells  OPCs  which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin  we isolated sp7  mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs  chondrogenic mesenchymal progenitors CMPs  and osteoblasts.", null, "pubmed:38193362", null, "EGFP+/sp7   CMP  rep1", "GSM7987443", null, "source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Chondrogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing", "EGFP+/sp7   CMP  rep1", "High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id  length  Genbank id  RNA type  gene name  product  raw count  RPKM and TPM values.", "14 dpa adult caudal fin", "Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer\u2019s protocol.", "Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 \u00b0C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.", "tissue:14 dpa adult caudal fin|cell type:Chondrogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry", "GSM7987443", "GSM7987443: EGFP+/sp7   CMP  rep1; Danio rerio; RNA Seq", "GSM7987443 r1", "GSM7987443", "1", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP479308", null, null, "Mes-G_S15_R1_001.fastq.gz Mes-G_S15_R2_001.fastq.gz", "fastq fastq", 5321588000.0, 13303970.0, "GSM7987443 r1", "0:200 1:200", "A:1405233304;C:1195662643;G:1342003810;T:1376732727;N:1955516", 200, 200, null, null, 1405233304, 1195662643, 1342003810, 1376732727, 1955516, "SRX22985576", "SRS19950786", "SRA1773396", "Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology", "Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology", 2, 0.00961, 0.02419, 0.00032, 0.00052, 0.9945, 0.99324, 0.51073, 0.48429, 200, 200, "T", "T", "mates < 9% mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2023-12-20", "Adult", "Adult", "Fin", "Surface Structure"], [30628, "SRR27942672", "SRX23599456", "SRS20442304", "SRP489317", "PRJNA1075480", "Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution", "PRJNA1075480", "Other", "Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. 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Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.", null, "pubmed:39809530", null, "6 day post amputation replicate 1", "6dpa fin1", null, "strain:Tgsp7:EGFP|age:1 year|collection date:2022 02 04|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:6 day post amputation replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "6dpa fin1 snRNA", "6dpa1 RNA", "6dpa1 RNA", "Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP489317", null, null, "6dpa1-GEX-lib1_S1_L001_R2_001.fastq.gz 6dpa1-GEX-lib1_S1_L001_R1_001.fastq.gz", "fastq fastq", 106483322870.0, 598220915.0, "6dpa1 GEX lib1 S1 L001 R1 001.fastq.gz", "0:28 1:150", "A:32833929738;C:22259209515;G:23233729505;T:28155235335;N:1218777", 28, 150, null, null, 32833929738, 22259209515, 23233729505, 28155235335, 1218777, "SRX23599455", "SRS20442303", "SRA1801018", "Washington University in St. Louis School of Medicine|Genetics", "Washington University in St. Louis School of Medicine", 2, 0.02691, 0.87324, 0.01263, 0.22013, 0.98415, 0.83144, 0.4808, 0.62463, 28, 150, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-02-12", "Adult", "Adult", "Fin", "Surface Structure"], [30630, "SRR27942674", "SRX23599454", "SRS20442302", "SRP489317", "PRJNA1075480", "Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution", "PRJNA1075480", "Other", "Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.", null, "pubmed:39809530", null, "4 day post amputation replicate 2", "4dpa fin2", null, "strain:Tgsp7:EGFP|age:1 year|collection date:2022 01 12|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:4 day post amputation replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "4dpa fin2 snRNA", "4dpa2 RNA", "4dpa2 RNA", "Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP489317", null, null, "4dpa2-GEX-lib1_S2_L002_R1_001.fastq.gz 4dpa2-GEX-lib1_S2_L002_R2_001.fastq.gz", "fastq fastq", 100355045420.0, 563792390.0, "4dpa2 GEX lib1 S2 L002 R1 001.fastq.gz", "0:28 1:150", "A:30110360316;C:21497825420;G:22061747902;T:26684746811;N:364971", 28, 150, null, null, 30110360316, 21497825420, 22061747902, 26684746811, 364971, "SRX23599454", "SRS20442302", "SRA1801018", "Washington University in St. Louis School of Medicine|Genetics", "Washington University in St. Louis School of Medicine", 2, 0.02956, 0.90492, 0.01391, 0.21143, 0.98324, 0.82347, 0.46993, 0.73177, 28, 150, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-02-12", "Adult", "Adult", "Fin", "Surface Structure"], [30631, "SRR27942675", "SRX23599453", "SRS20442301", "SRP489317", "PRJNA1075480", "Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution", "PRJNA1075480", "Other", "Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.", null, "pubmed:39809530", null, "4 day post amputation replicate 1", "4dpa fin1", null, "strain:Tgsp7:EGFP|age:1 year|collection date:2021 11 22|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:4 day post amputation replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "4dpa fin1 snRNA", "4dpa1 RNA", "4dpa1 RNA", "Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP489317", null, null, "4dpa1-GEX-lib1_S1_L002_R2_001.fastq.gz 4dpa1-GEX-lib1_S1_L002_R1_001.fastq.gz", "fastq fastq", 104945766346.0, 589582957.0, "4dpa1 GEX lib1 S1 L002 R1 001.fastq.gz", "0:28 1:150", "A:32489394291;C:21756067815;G:22868928766;T:27829952922;N:1422552", 28, 150, null, null, 32489394291, 21756067815, 22868928766, 27829952922, 1422552, "SRX23599453", "SRS20442301", "SRA1801018", "Washington University in St. Louis School of Medicine|Genetics", "Washington University in St. Louis School of Medicine", 2, 0.02921, 0.86985, 0.01399, 0.22211, 0.98372, 0.8294, 0.45783, 0.71655, 28, 150, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-02-12", "Adult", "Adult", "Fin", "Surface Structure"], [30632, "SRR27942676", "SRX23599452", "SRS20442300", "SRP489317", "PRJNA1075480", "Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution", "PRJNA1075480", "Other", "Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.", null, "pubmed:39809530", null, "2 day post amputation replicate 2", "2dpa fin2", null, "strain:Tgsp7:EGFP|age:1 year|collection date:2022 01 12|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:2 day post amputation replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "2dpa fin2 snRNA", "2dpa2 RNA", "2dpa2 RNA", "Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP489317", null, null, "2dpa2-GEX-lib1_S1_L001_R2_001.fastq.gz 2dpa2-GEX-lib1_S1_L001_R1_001.fastq.gz", "fastq fastq", 84977307334.0, 477400603.0, "2dpa2 GEX lib1 S1 L001 R1 001.fastq.gz", "0:28 1:150", "A:25498895454;C:18439149160;G:19015549944;T:22023275686;N:437090", 28, 150, null, null, 25498895454, 18439149160, 19015549944, 22023275686, 437090, "SRX23599452", "SRS20442300", "SRA1801018", "Washington University in St. Louis School of Medicine|Genetics", "Washington University in St. Louis School of Medicine", 2, 0.02811, 0.91493, 0.01297, 0.18571, 0.98492, 0.83554, 0.4671, 0.75085, 28, 150, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-02-12", "Adult", "Adult", "Fin", "Surface Structure"], [30633, "SRR27942677", "SRX23599451", "SRS20442299", "SRP489317", "PRJNA1075480", "Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution", "PRJNA1075480", "Other", "Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. 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Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.", null, "pubmed:39809530", null, "1 day post amputation replicate 2", "1dpa fin2", null, "strain:Tgsp7:EGFP|age:1 year|collection date:2022 01 27|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:1 day post amputation replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "1dpa fin2 snRNA", "1dpa2 RNA", "1dpa2 RNA", "Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP489317", null, null, "1dpa2-GEX-lib1_S1_L004_R1_001.fastq.gz 1dpa2-GEX-lib1_S1_L004_R2_001.fastq.gz", "fastq fastq", 84562055050.0, 475067725.0, "1dpa2 GEX lib1 S1 L004 R1 001.fastq.gz", "0:28 1:150", "A:25830017026;C:17874013165;G:18722117096;T:22135719607;N:188156", 28, 150, null, null, 25830017026, 17874013165, 18722117096, 22135719607, 188156, "SRX23599450", "SRS20442298", "SRA1801018", "Washington University in St. Louis School of Medicine|Genetics", "Washington University in St. Louis School of Medicine", 2, 0.02723, 0.88745, 0.01218, 0.18561, 0.98573, 0.83613, 0.45958, 0.63016, 28, 150, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-02-12", "Adult", "Adult", "Fin", "Surface Structure"], [30635, "SRR27942679", "SRX23599449", "SRS20442297", "SRP489317", "PRJNA1075480", "Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution", "PRJNA1075480", "Other", "Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. 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Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.", null, "pubmed:39809530", null, "0 day post amputation replicate 2", "0dpa fin2", null, "strain:Tgsp7:EGFP|age:1 year|collection date:2022 01 27|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:0 day post amputation replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "0dpa fin2 snRNA", "0dpa2 RNA", "0dpa2 RNA", "Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP489317", null, null, "0dpa2-GEX-lib1_S2_L004_R2_001.fastq.gz 0dpa2-GEX-lib1_S2_L004_R1_001.fastq.gz", "fastq fastq", 94016384252.0, 528181934.0, "0dpa2 GEX lib1 S2 L004 R1 001.fastq.gz", "0:28 1:150", "A:28851000041;C:19680536935;G:20640186670;T:24844451695;N:208911", 28, 150, null, null, 28851000041, 19680536935, 20640186670, 24844451695, 208911, "SRX23599438", "SRS20442296", "SRA1801018", "Washington University in St. Louis School of Medicine|Genetics", "Washington University in St. Louis School of Medicine", 2, 0.02684, 0.87686, 0.01274, 0.21544, 0.98703, 0.85975, 0.45722, 0.74164, 28, 150, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-02-12", "Adult", "Adult", "Fin", "Surface Structure"], [30637, "SRR27942691", "SRX23599437", "SRS20442295", "SRP489317", "PRJNA1075480", "Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution", "PRJNA1075480", "Other", "Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.", null, "pubmed:39809530", null, "0 day post amputation replicate 1", "0dpa fin1", null, "strain:Tgsp7:EGFP|age:1 year|collection date:2021 07 26|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:0 day post amputation replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "0dpa fin1 snRNA", "0dpa1 RNA", "0dpa1 RNA", "Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP489317", null, null, "0dpa1-GEX-lib1_S1_L001_R1_001.fastq.gz 0dpa1-GEX-lib1_S1_L001_R2_001.fastq.gz", "fastq fastq", 95106992388.0, 534308946.0, "0dpa1 GEX lib1 S1 L001 R1 001.fastq.gz", "0:28 1:150", "A:29570202174;C:19531427210;G:20167731244;T:25836092390;N:1539370", 28, 150, null, null, 29570202174, 19531427210, 20167731244, 25836092390, 1539370, "SRX23599437", "SRS20442295", "SRA1801018", "Washington University in St. Louis School of Medicine|Genetics", "Washington University in St. Louis School of Medicine", 2, 0.02388, 0.87039, 0.01162, 0.24031, 0.98652, 0.85354, 0.48963, 0.74378, 28, 150, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-02-12", "Adult", "Adult", "Fin", "Surface Structure"], [32858, "SRR29482326", "SRX24993370", "SRS21694834", "SRP515140", "PRJNA1126247", "Specific oncogene activation of the cell of origin in mucosal melanoma [SORT seq]", "GSE270356", "Other", "Mucosal melanoma MM is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics  we develop a zebrafish model in which all melanocytes experience CCND1 expression and loss of PTEN and TP53. Surprisingly  melanoma only develops from melanocytes lining internal organs  analogous to the location of patient MM. We find that zebrafish MMs have a unique chromatin landscape from cutaneous melanoma. Internal melanocytes are labeled using a MM specific transcriptional enhancer. Normal zebrafish internal melanocytes share a gene expression signature with MMs. Patient and zebrafish MMs show increased migratory neural crest gene and decreased antigen presentation gene expression  consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors  allowing this model to be used for MM therapeutic discovery. As this is a non MAPK driven genetically engineered model of melanoma  our work also has implications for the 15% of cutaneous melanoma patients who lack MAPK driving mutations.  Overall design: Single cell RNA sequencing was done on internal vs. external normal adult zebrafish melanocytes using the SORT seq platform.", null, null, null, "Internal melanocytes", "GSM8340241", null, "source name:Internal melanocytes|tissue:Internal melanocytes|cell type:melanocytes|genotype:mitfa / ; roy /  fish injected with mitfa:GFP|geo loc name:missing|collection date:missing", "Internal melanocytes", "BWA was used to align paired end read to danRer11. Count tables were generated using MapAndGo. Count tables were corrected using UMI to remove duplicate reads. Transcript counts were adjusted using Poissonian counting statistics to yield the number of UMIs detected per cell. Counts were imported into R using the Seurat suite version 3.0 Assembly: danRer11 Supplementary files format and content: .tsv file contains count matrix file used for data normalization and visualization using Seurat Library strategy: SORT seq", "Internal melanocytes", null, "Respective tissues were mechanically dissociated  digested in TrypLE for 45 min Invitrogen  12563011  40uM filtered  spun down  and resuspended in FACs buffer dPBS Mg+/Ca+ free  with 2% FBS  pen/strep. Cells were heat lysed at 65\u00b0C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification  library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.", "mitfa / ; roy /  zebrafish injected with mitfa:GFP were Raised to maturity to obtain tissues", "tissue:Internal melanocytes|cell type:melanocytes|genotype:mitfa / ; roy /  fish injected with mitfa:GFP", "GSM8340241", "GSM8340241: Internal melanocytes; Danio rerio; OTHER", "GSM8340241 r1", "GSM8340241", "1", "Respective tissues were mechanically dissociated  digested in TrypLE for 45 min Invitrogen  12563011  40uM filtered  spun down  and resuspended in FACs buffer dPBS Mg+/Ca+ free  with 2% FBS  pen/strep. Cells were heat lysed at 65\u00b0C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification  library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP515140", null, null, "HAR-MI-002_H5GCWBGXF_R2.fastq.gz HAR-MI-002_H5GCWBGXF_R1.fastq.gz", "fastq fastq", 2957975418.0, 34395063.0, "GSM8340241 r1", "0:26 1:60", "A:738954503;C:560052455;G:520746060;T:1137116132;N:1106268", 26, 60, null, null, 738954503, 560052455, 520746060, 1137116132, 1106268, "SRX24993370", "SRS21694834", "SRA1904773", "Insco Lab, Medical Oncology, Dana Farber Cancer Institute", "Insco Lab, Medical Oncology, Dana Farber Cancer Institute", 2, 0.11637, 0.84116, 0.10894, 0.31188, 0.98851, 0.71526, 0.6688, 0.60221, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "United States", "2024-06-20", "Undetermined", "Adult", "Skin", "Surface Structure"], [32859, "SRR29482327", "SRX24993369", "SRS21694833", "SRP515140", "PRJNA1126247", "Specific oncogene activation of the cell of origin in mucosal melanoma [SORT seq]", "GSE270356", "Other", "Mucosal melanoma MM is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics  we develop a zebrafish model in which all melanocytes experience CCND1 expression and loss of PTEN and TP53. Surprisingly  melanoma only develops from melanocytes lining internal organs  analogous to the location of patient MM. We find that zebrafish MMs have a unique chromatin landscape from cutaneous melanoma. Internal melanocytes are labeled using a MM specific transcriptional enhancer. Normal zebrafish internal melanocytes share a gene expression signature with MMs. Patient and zebrafish MMs show increased migratory neural crest gene and decreased antigen presentation gene expression  consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors  allowing this model to be used for MM therapeutic discovery. As this is a non MAPK driven genetically engineered model of melanoma  our work also has implications for the 15% of cutaneous melanoma patients who lack MAPK driving mutations.  Overall design: Single cell RNA sequencing was done on internal vs. external normal adult zebrafish melanocytes using the SORT seq platform.", null, null, null, "Cutaneous melanocytes", "GSM8340240", null, "source name:Cutaneous melanocytes|tissue:Cutaneous melanocytes|cell type:melanocytes|genotype:mitfa / ; roy /  fish injected with mitfa:GFP|geo loc name:missing|collection date:missing", "Cutaneous melanocytes", "BWA was used to align paired end read to danRer11. Count tables were generated using MapAndGo. Count tables were corrected using UMI to remove duplicate reads. Transcript counts were adjusted using Poissonian counting statistics to yield the number of UMIs detected per cell. Counts were imported into R using the Seurat suite version 3.0 Assembly: danRer11 Supplementary files format and content: .tsv file contains count matrix file used for data normalization and visualization using Seurat Library strategy: SORT seq", "Cutaneous melanocytes", null, "Respective tissues were mechanically dissociated  digested in TrypLE for 45 min Invitrogen  12563011  40uM filtered  spun down  and resuspended in FACs buffer dPBS Mg+/Ca+ free  with 2% FBS  pen/strep. Cells were heat lysed at 65\u00b0C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification  library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.", "mitfa / ; roy /  zebrafish injected with mitfa:GFP were Raised to maturity to obtain tissues", "tissue:Cutaneous melanocytes|cell type:melanocytes|genotype:mitfa / ; roy /  fish injected with mitfa:GFP", "GSM8340240", "GSM8340240: Cutaneous melanocytes; Danio rerio; OTHER", "GSM8340240 r1", "GSM8340240", "1", "Respective tissues were mechanically dissociated  digested in TrypLE for 45 min Invitrogen  12563011  40uM filtered  spun down  and resuspended in FACs buffer dPBS Mg+/Ca+ free  with 2% FBS  pen/strep. Cells were heat lysed at 65\u00b0C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification  library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP515140", null, null, "HAR-MI-001_H5GCWBGXF_R2.fastq.gz HAR-MI-001_H5GCWBGXF_R1.fastq.gz", "fastq fastq", 2680460212.0, 31168142.0, "GSM8340240 r1", "0:26 1:60", "A:704357434;C:519158361;G:467098420;T:988838604;N:1007393", 26, 60, null, null, 704357434, 519158361, 467098420, 988838604, 1007393, "SRX24993369", "SRS21694833", "SRA1904773", "Insco Lab, Medical Oncology, Dana Farber Cancer Institute", "Insco Lab, Medical Oncology, Dana Farber Cancer Institute", 2, 0.11679, 0.81545, 0.10693, 0.5033, 0.9808, 0.76404, 0.44749, 0.57623, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "United States", "2024-06-20", "Undetermined", "Adult", "Skin", 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"Northwest A&F University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-09-22", "Adult", "Adult", "Skin", "Surface Structure"], [33843, "SRR30763640", "SRX26165993", "SRS22710774", "SRP534093", "PRJNA1163532", "Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus", "PRJNA1163532", "Whole Genome Sequencing", null, null, null, null, "Skin 1dpi2", "Skin 1d 3", null, "breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 1dpi 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish skin   RNA seq  Skin 1d 3", "SK 1D 3", "SK 1D 3", "Zebrafish skin at 1 dpv post immunization with glycoprotein of spring viraemia of carp virus", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP534093", null, null, "Skin_1dpi2_Clean_Data1.fq.gz Skin_1dpi2_Clean_Data2.fq.gz", "fastq fastq", 6317753535.0, 22527726.0, "Skin 1dpi2 Clean Data1.fq.gz", "0:140.23 1:140.22", "A:1637469629;C:1508203339;G:1526532646;T:1645411954;N:135967", 140, 140, null, null, 1637469629, 1508203339, 1526532646, 1645411954, 135967, "SRX26165993", "SRS22710774", "SRA1977051", "Northwest A&amp;F University|College of Animal Science and Technology", "Northwest A&F University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-09-22", "Adult", "Adult", "Skin", "Surface Structure"], [33844, "SRR30763641", "SRX26165992", "SRS22710773", "SRP534093", "PRJNA1163532", "Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus", "PRJNA1163532", "Whole Genome Sequencing", null, null, null, null, "Skin 1dpi1", "Skin 1d 2", null, "breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 1dpi 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish skin   RNA seq  Skin 1d 2", "SK 1D 2", "SK 1D 2", "Zebrafish skin at 1 dpv post immunization with glycoprotein of spring viraemia of carp virus", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP534093", null, null, "Skin_1dpi1_Clean_Data1.fq.gz Skin_1dpi1_Clean_Data2.fq.gz", "fastq fastq", 5665401221.0, 20209478.0, "Skin 1dpi1 Clean Data1.fq.gz", "0:140.17 1:140.16", "A:1463485728;C:1359900876;G:1372085350;T:1469804976;N:124291", 140, 140, null, null, 1463485728, 1359900876, 1372085350, 1469804976, 124291, "SRX26165992", "SRS22710773", "SRA1977051", "Northwest A&amp;F University|College of Animal Science and Technology", "Northwest A&F University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-09-22", "Adult", "Adult", "Skin", "Surface Structure"], [33845, "SRR30763642", "SRX26165991", "SRS22710772", "SRP534093", "PRJNA1163532", "Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus", "PRJNA1163532", "Whole Genome Sequencing", null, null, null, null, "Skin 1dpi", "Skin 1d 1", null, "breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 1dpi 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish skin   RNA seq  Skin 1d 1", "SK 1D 1", "SK 1D 1", "Zebrafish skin at 1 dpv post immunization with glycoprotein of spring viraemia of carp virus", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP534093", null, null, "Skin_1dpi_Clean_Data1.fq.gz Skin_1dpi_Clean_Data2.fq.gz", "fastq fastq", 4758945020.0, 17104843.0, "Skin 1dpi Clean Data1.fq.gz", "0:139.12 1:139.11", "A:1261511064;C:1113177324;G:1128285977;T:1255959998;N:10657", 139, 139, null, null, 1261511064, 1113177324, 1128285977, 1255959998, 10657, "SRX26165991", "SRS22710772", "SRA1977051", "Northwest A&amp;F University|College of Animal Science and Technology", "Northwest A&F University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-09-22", "Adult", "Adult", "Skin", "Surface Structure"], [34153, "SRR31377592", "SRX26751157", "SRS23239770", "SRP545865", "PRJNA1187491", "CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.", "GSE282155", "Transcriptome Analysis", "CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, null, null, "CCSER1 S Body R6", "GSM8637009", null, "source name:whole body|tissue:whole body|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing", "CCSER1 S Body R6", "Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned", "whole body", null, "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "tissue:whole body|genotype:CCSER1 S48Y*", "GSM8637009", "GSM8637009: CCSER1 S Body R6; Danio rerio; RNA Seq", "GSM8637009 r1", "GSM8637009", "1", "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP545865", null, null, "RZW041_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW041_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 3891217754.0, 12884827.0, "GSM8637009 r1", "0:151 1:151", "A:1016852836;C:927774615;G:947465133;T:998741423;N:383747", 151, 151, null, null, 1016852836, 927774615, 947465133, 998741423, 383747, "SRX26751157", "SRS23239770", "SRA2016812", "ASM Lab, Physiology, NUS", "ASM Lab, Physiology, NUS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2024-11-18", "Undetermined", "Adult", "Trunk", "Surface Structure"], [34154, "SRR31377593", "SRX26751156", "SRS23239769", "SRP545865", "PRJNA1187491", "CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.", "GSE282155", "Transcriptome Analysis", "CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, null, null, "CCSER1 S Body R5", "GSM8637008", null, "source name:whole body|tissue:whole body|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing", "CCSER1 S Body R5", "Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned", "whole body", null, "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "tissue:whole body|genotype:CCSER1 S48Y*", "GSM8637008", "GSM8637008: CCSER1 S Body R5; Danio rerio; RNA Seq", "GSM8637008 r1", "GSM8637008", "1", "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP545865", null, null, "RZW040_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW040_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 3646264950.0, 12073725.0, "GSM8637008 r1", "0:151 1:151", "A:939260848;C:884661915;G:900614466;T:921376437;N:351284", 151, 151, null, null, 939260848, 884661915, 900614466, 921376437, 351284, "SRX26751156", "SRS23239769", "SRA2016812", "ASM Lab, Physiology, NUS", "ASM Lab, Physiology, NUS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2024-11-18", "Undetermined", "Adult", "Trunk", "Surface Structure"], [34155, "SRR31377594", "SRX26751155", "SRS23239768", "SRP545865", "PRJNA1187491", "CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.", "GSE282155", "Transcriptome Analysis", "CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, null, null, "CCSER1 S Body R4", "GSM8637007", null, "source name:whole body|tissue:whole body|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing", "CCSER1 S Body R4", "Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned", "whole body", null, "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "tissue:whole body|genotype:CCSER1 S48Y*", "GSM8637007", "GSM8637007: CCSER1 S Body R4; Danio rerio; RNA Seq", "GSM8637007 r1", "GSM8637007", "1", "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP545865", null, null, "RZW039_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW039_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 4173716406.0, 13820253.0, "GSM8637007 r1", "0:151 1:151", "A:1101647100;C:985852757;G:1008447663;T:1077356024;N:412862", 151, 151, null, null, 1101647100, 985852757, 1008447663, 1077356024, 412862, "SRX26751155", "SRS23239768", "SRA2016812", "ASM Lab, Physiology, NUS", "ASM Lab, Physiology, NUS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2024-11-18", "Undetermined", "Adult", "Trunk", "Surface Structure"], [34156, "SRR31377595", "SRX26751154", "SRS23239766", "SRP545865", "PRJNA1187491", "CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.", "GSE282155", "Transcriptome Analysis", "CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, null, null, "CCSER1 S Body R3", "GSM8637006", null, "source name:whole body|tissue:whole body|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing", "CCSER1 S Body R3", "Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned", "whole body", null, "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "tissue:whole body|genotype:CCSER1 S48Y*", "GSM8637006", "GSM8637006: CCSER1 S Body R3; Danio rerio; RNA Seq", "GSM8637006 r1", "GSM8637006", "1", "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP545865", null, null, "RZW038_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW038_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 4042195708.0, 13384754.0, "GSM8637006 r1", "0:151 1:151", "A:1060347597;C:961319252;G:982742171;T:1037395227;N:391461", 151, 151, null, null, 1060347597, 961319252, 982742171, 1037395227, 391461, "SRX26751154", "SRS23239766", "SRA2016812", "ASM Lab, Physiology, NUS", "ASM Lab, Physiology, NUS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2024-11-18", "Undetermined", "Adult", "Trunk", "Surface Structure"], [34157, "SRR31377596", "SRX26751153", "SRS23239767", "SRP545865", "PRJNA1187491", "CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.", "GSE282155", "Transcriptome Analysis", "CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, null, null, "CCSER1 S Body R2", "GSM8637005", null, "source name:whole body|tissue:whole body|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing", "CCSER1 S Body R2", "Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned", "whole body", null, "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "tissue:whole body|genotype:CCSER1 S48Y*", "GSM8637005", "GSM8637005: CCSER1 S Body R2; Danio rerio; RNA Seq", "GSM8637005 r1", "GSM8637005", "1", "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP545865", null, null, "RZW037_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW037_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 4273642468.0, 14151134.0, "GSM8637005 r1", "0:151 1:151", "A:1128762921;C:1007923026;G:1029470831;T:1107066433;N:419257", 151, 151, null, null, 1128762921, 1007923026, 1029470831, 1107066433, 419257, "SRX26751153", "SRS23239767", "SRA2016812", "ASM Lab, Physiology, NUS", "ASM Lab, Physiology, NUS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2024-11-18", "Undetermined", "Adult", "Trunk", "Surface Structure"], [34158, "SRR31377597", "SRX26751152", "SRS23239764", "SRP545865", "PRJNA1187491", "CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.", "GSE282155", "Transcriptome Analysis", "CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, null, null, "CCSER1 S Body R1", "GSM8637004", null, "source name:whole body|tissue:whole body|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing", "CCSER1 S Body R1", "Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned", "whole body", null, "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "tissue:whole body|genotype:CCSER1 S48Y*", "GSM8637004", "GSM8637004: CCSER1 S Body R1; Danio rerio; RNA Seq", "GSM8637004 r1", "GSM8637004", "1", "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP545865", null, null, "RZW036_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW036_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 3653975010.0, 12099255.0, "GSM8637004 r1", "0:151 1:151", "A:955600414;C:873541559;G:890489547;T:933988860;N:354630", 151, 151, null, null, 955600414, 873541559, 890489547, 933988860, 354630, "SRX26751152", "SRS23239764", "SRA2016812", "ASM Lab, Physiology, NUS", "ASM Lab, Physiology, NUS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2024-11-18", "Undetermined", "Adult", "Trunk", "Surface Structure"], [34159, "SRR31377598", "SRX26751151", "SRS23239765", "SRP545865", "PRJNA1187491", "CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.", "GSE282155", "Transcriptome Analysis", "CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, null, null, "CCSER1 M Body R6", "GSM8637003", null, "source name:whole body|tissue:whole body|genotype:CCSER1 P471|geo loc name:missing|collection date:missing", "CCSER1 M Body R6", "Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned", "whole body", null, "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "tissue:whole body|genotype:CCSER1 P471", "GSM8637003", "GSM8637003: CCSER1 M Body R6; Danio rerio; RNA Seq", "GSM8637003 r1", "GSM8637003", "1", "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP545865", null, null, "RZW035_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW035_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 4080528266.0, 13511683.0, "GSM8637003 r1", "0:151 1:151", "A:1061173416;C:977476934;G:997386836;T:1044093823;N:397257", 151, 151, null, null, 1061173416, 977476934, 997386836, 1044093823, 397257, "SRX26751151", "SRS23239765", "SRA2016812", "ASM Lab, Physiology, NUS", "ASM Lab, Physiology, NUS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2024-11-18", "Undetermined", "Adult", "Trunk", "Surface Structure"], [34160, "SRR31377599", "SRX26751150", "SRS23239762", "SRP545865", "PRJNA1187491", "CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.", "GSE282155", "Transcriptome Analysis", "CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, null, null, "CCSER1 M Body R5", "GSM8637002", null, "source name:whole body|tissue:whole body|genotype:CCSER1 P471|geo loc name:missing|collection date:missing", "CCSER1 M Body R5", "Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned", "whole body", null, "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "tissue:whole body|genotype:CCSER1 P471", "GSM8637002", "GSM8637002: CCSER1 M Body R5; Danio rerio; RNA Seq", "GSM8637002 r1", "GSM8637002", "1", "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP545865", null, null, "RZW034_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW034_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 4337490402.0, 14362551.0, "GSM8637002 r1", "0:151 1:151", "A:1123121935;C:1047421198;G:1062576487;T:1103949606;N:421176", 151, 151, null, null, 1123121935, 1047421198, 1062576487, 1103949606, 421176, "SRX26751150", "SRS23239762", "SRA2016812", "ASM Lab, Physiology, NUS", "ASM Lab, Physiology, NUS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2024-11-18", "Undetermined", "Adult", "Trunk", "Surface Structure"], [34161, "SRR31377600", "SRX26751149", "SRS23239760", "SRP545865", "PRJNA1187491", "CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.", "GSE282155", "Transcriptome Analysis", "CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, null, null, "CCSER1 M Body R4", "GSM8637001", null, "source name:whole body|tissue:whole body|genotype:CCSER1 P471|geo loc name:missing|collection date:missing", "CCSER1 M Body R4", "Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned", "whole body", null, "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "tissue:whole body|genotype:CCSER1 P471", "GSM8637001", "GSM8637001: CCSER1 M Body R4; Danio rerio; RNA Seq", "GSM8637001 r1", "GSM8637001", "1", "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP545865", null, null, "RZW033_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW033_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 3844091862.0, 12728781.0, "GSM8637001 r1", "0:151 1:151", "A:991817790;C:930869770;G:945916630;T:975114794;N:372878", 151, 151, null, null, 991817790, 930869770, 945916630, 975114794, 372878, "SRX26751149", "SRS23239760", "SRA2016812", "ASM Lab, Physiology, NUS", "ASM Lab, Physiology, NUS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2024-11-18", "Undetermined", "Adult", "Trunk", "Surface Structure"], [34162, "SRR31377601", "SRX26751148", "SRS23239763", "SRP545865", "PRJNA1187491", "CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.", "GSE282155", "Transcriptome Analysis", "CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, null, null, "CCSER1 M Body R3", "GSM8637000", null, "source name:whole body|tissue:whole body|genotype:CCSER1 P471|geo loc name:missing|collection date:missing", "CCSER1 M Body R3", "Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned", "whole body", null, "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "tissue:whole body|genotype:CCSER1 P471", "GSM8637000", "GSM8637000: CCSER1 M Body R3; Danio rerio; RNA Seq", "GSM8637000 r1", "GSM8637000", "1", "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP545865", null, null, "RZW032_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW032_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 3561535830.0, 11793165.0, "GSM8637000 r1", "0:151 1:151", "A:925501870;C:854996726;G:868955460;T:911732180;N:349594", 151, 151, null, null, 925501870, 854996726, 868955460, 911732180, 349594, "SRX26751148", "SRS23239763", "SRA2016812", "ASM Lab, Physiology, NUS", "ASM Lab, Physiology, NUS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2024-11-18", "Undetermined", "Adult", "Trunk", "Surface Structure"], [34163, "SRR31377602", "SRX26751147", "SRS23239761", "SRP545865", "PRJNA1187491", "CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.", "GSE282155", "Transcriptome Analysis", "CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, null, null, "CCSER1 M Body R2", "GSM8636999", null, "source name:whole body|tissue:whole body|genotype:CCSER1 P471|geo loc name:missing|collection date:missing", "CCSER1 M Body R2", "Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned", "whole body", null, "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "tissue:whole body|genotype:CCSER1 P471", "GSM8636999", "GSM8636999: CCSER1 M Body R2; Danio rerio; RNA Seq", "GSM8636999 r1", "GSM8636999", "1", "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP545865", null, null, "RZW031_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW031_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 4010996088.0, 13281444.0, "GSM8636999 r1", "0:151 1:151", "A:1041141909;C:965136690;G:981220550;T:1023106736;N:390203", 151, 151, null, null, 1041141909, 965136690, 981220550, 1023106736, 390203, "SRX26751147", "SRS23239761", "SRA2016812", "ASM Lab, Physiology, NUS", "ASM Lab, Physiology, NUS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2024-11-18", "Undetermined", "Adult", "Trunk", "Surface Structure"], [34164, "SRR31377603", "SRX26751146", "SRS23239759", "SRP545865", "PRJNA1187491", "CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.", "GSE282155", "Transcriptome Analysis", "CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, null, null, "CCSER1 M Body R1", "GSM8636998", null, "source name:whole body|tissue:whole body|genotype:CCSER1 P471|geo loc name:missing|collection date:missing", "CCSER1 M Body R1", "Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned", "whole body", null, "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "tissue:whole body|genotype:CCSER1 P471", "GSM8636998", "GSM8636998: CCSER1 M Body R1; Danio rerio; RNA Seq", "GSM8636998 r1", "GSM8636998", "1", "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP545865", null, null, "RZW030_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW030_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 3897705620.0, 12906310.0, "GSM8636998 r1", "0:151 1:151", "A:1018200154;C:931829100;G:950742174;T:996554508;N:379684", 151, 151, null, null, 1018200154, 931829100, 950742174, 996554508, 379684, "SRX26751146", "SRS23239759", "SRA2016812", "ASM Lab, Physiology, NUS", "ASM Lab, Physiology, NUS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2024-11-18", "Undetermined", "Adult", "Trunk", "Surface Structure"], [34165, "SRR31377604", "SRX26751145", "SRS23239758", "SRP545865", "PRJNA1187491", "CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.", "GSE282155", "Transcriptome Analysis", "CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, null, null, "WT Body R6", "GSM8636997", null, "source name:whole body|tissue:whole body|genotype:WT|geo loc name:missing|collection date:missing", "WT Body R6", "Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned", "whole body", null, "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "tissue:whole body|genotype:WT", "GSM8636997", "GSM8636997: WT Body R6; Danio rerio; RNA Seq", "GSM8636997 r1", "GSM8636997", "1", "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP545865", null, null, "RZW029_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW029_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 3865866666.0, 12800883.0, "GSM8636997 r1", "0:151 1:151", "A:1011251980;C:922495324;G:940649850;T:991092479;N:377033", 151, 151, null, null, 1011251980, 922495324, 940649850, 991092479, 377033, "SRX26751145", "SRS23239758", "SRA2016812", "ASM Lab, Physiology, NUS", "ASM Lab, Physiology, NUS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2024-11-18", "Undetermined", "Adult", "Trunk", "Surface Structure"], [34166, "SRR31377605", "SRX26751144", "SRS23239756", "SRP545865", "PRJNA1187491", "CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.", "GSE282155", "Transcriptome Analysis", "CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, null, null, "WT Body R5", "GSM8636996", null, "source name:whole body|tissue:whole body|genotype:WT|geo loc name:missing|collection date:missing", "WT Body R5", "Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned", "whole body", null, "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "tissue:whole body|genotype:WT", "GSM8636996", "GSM8636996: WT Body R5; Danio rerio; RNA Seq", "GSM8636996 r1", "GSM8636996", "1", "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP545865", null, null, "RZW028_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW028_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 4063620192.0, 13455696.0, "GSM8636996 r1", "0:151 1:151", "A:1059319911;C:972296744;G:990411694;T:1041199642;N:392201", 151, 151, null, null, 1059319911, 972296744, 990411694, 1041199642, 392201, "SRX26751144", "SRS23239756", "SRA2016812", "ASM Lab, Physiology, NUS", "ASM Lab, Physiology, NUS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2024-11-18", "Undetermined", "Adult", "Trunk", "Surface Structure"], [34167, "SRR31377606", "SRX26751143", "SRS23239757", "SRP545865", "PRJNA1187491", "CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.", "GSE282155", "Transcriptome Analysis", "CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, null, null, "WT Body R4", "GSM8636995", null, "source name:whole body|tissue:whole body|genotype:WT|geo loc name:missing|collection date:missing", "WT Body R4", "Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned", "whole body", null, "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "tissue:whole body|genotype:WT", "GSM8636995", "GSM8636995: WT Body R4; Danio rerio; RNA Seq", "GSM8636995 r1", "GSM8636995", "1", "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP545865", null, null, "RZW027_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW027_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 3813832368.0, 12628584.0, "GSM8636995 r1", "0:151 1:151", "A:1000392936;C:909932334;G:925952997;T:977190341;N:363760", 151, 151, null, null, 1000392936, 909932334, 925952997, 977190341, 363760, "SRX26751143", "SRS23239757", "SRA2016812", "ASM Lab, Physiology, NUS", "ASM Lab, Physiology, NUS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2024-11-18", "Undetermined", "Adult", "Trunk", "Surface Structure"], [34168, "SRR31377607", "SRX26751142", "SRS23239754", "SRP545865", "PRJNA1187491", "CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.", "GSE282155", "Transcriptome Analysis", "CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, null, null, "WT Body R3", "GSM8636994", null, "source name:whole body|tissue:whole body|genotype:WT|geo loc name:missing|collection date:missing", "WT Body R3", "Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned", "whole body", null, "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "tissue:whole body|genotype:WT", "GSM8636994", "GSM8636994: WT Body R3; Danio rerio; RNA Seq", "GSM8636994 r1", "GSM8636994", "1", "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP545865", null, null, "RZW026_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW026_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 4006681716.0, 13267158.0, "GSM8636994 r1", "0:151 1:151", "A:1048048089;C:954759070;G:972606862;T:1030876175;N:391520", 151, 151, null, null, 1048048089, 954759070, 972606862, 1030876175, 391520, "SRX26751142", "SRS23239754", "SRA2016812", "ASM Lab, Physiology, NUS", "ASM Lab, Physiology, NUS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2024-11-18", "Undetermined", "Adult", "Trunk", "Surface Structure"], [34169, "SRR31377608", "SRX26751141", "SRS23239755", "SRP545865", "PRJNA1187491", "CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.", "GSE282155", "Transcriptome Analysis", "CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, null, null, "WT Body R2", "GSM8636993", null, "source name:whole body|tissue:whole body|genotype:WT|geo loc name:missing|collection date:missing", "WT Body R2", "Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned", "whole body", null, "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "tissue:whole body|genotype:WT", "GSM8636993", "GSM8636993: WT Body R2; Danio rerio; RNA Seq", "GSM8636993 r1", "GSM8636993", "1", "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP545865", null, null, "RZW025_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW025_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 4208402314.0, 13935107.0, "GSM8636993 r1", "0:151 1:151", "A:1096841306;C:1009718849;G:1025250660;T:1076184256;N:407243", 151, 151, null, null, 1096841306, 1009718849, 1025250660, 1076184256, 407243, "SRX26751141", "SRS23239755", "SRA2016812", "ASM Lab, Physiology, NUS", "ASM Lab, Physiology, NUS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2024-11-18", "Undetermined", "Adult", "Trunk", "Surface Structure"], [34170, "SRR31377609", "SRX26751140", "SRS23239752", "SRP545865", "PRJNA1187491", "CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.", "GSE282155", "Transcriptome Analysis", "CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, null, null, "WT Body R1", "GSM8636992", null, "source name:whole body|tissue:whole body|genotype:WT|geo loc name:missing|collection date:missing", "WT Body R1", "Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned", "whole body", null, "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "tissue:whole body|genotype:WT", "GSM8636992", "GSM8636992: WT Body R1; Danio rerio; RNA Seq", "GSM8636992 r1", "GSM8636992", "1", "The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP545865", null, null, "RZW024_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW024_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 4407394644.0, 14594022.0, "GSM8636992 r1", "0:151 1:151", "A:1153185021;C:1053968670;G:1069220613;T:1130594464;N:425876", 151, 151, null, null, 1153185021, 1053968670, 1069220613, 1130594464, 425876, "SRX26751140", "SRS23239752", "SRA2016812", "ASM Lab, Physiology, NUS", "ASM Lab, Physiology, NUS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2024-11-18", "Undetermined", "Adult", "Trunk", "Surface Structure"], [34294, "SRR31642040", "SRX27005496", "SRS23470018", "SRP550052", "PRJNA1195551", "scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint", "GSE283763", "Transcriptome Analysis", "Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.", null, null, null, "Jaw joint cells  70 dpjr  Single", "GSM8671781", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2|geo loc name:missing|collection date:missing", "Jaw joint cells  70 dpjr  Single", "CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files", "Jaw joint", "Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3\u2032 Library & Gel Bead Kit v2 10X Genomics  following the manufacturer\u2019s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.", null, "tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2", "GSM8671781", "GSM8671781: Jaw joint cells  70 dpjr  Single; Danio rerio; RNA Seq", "GSM8671781 r1", "GSM8671781", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3\u2032 Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP550052", null, "loader:fastq load.py", "70dpjr_Single_Animal_L002_I1_001.fastq.gz 70dpjr_Single_Animal_L002_I2_001.fastq.gz 70dpjr_Single_Animal_L002_R1_001.fastq.gz 70dpjr_Single_Animal_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 37049181954.0, 166888207.0, "GSM8671781 r1", "0:10 1:10 2:101 3:101", "A:9816927833;C:6602658028;G:6479430305;T:10811804702;N:596946", 10, 10, 101, 101, 9816927833, 6602658028, 6479430305, 10811804702, 596946, "SRX27005496", "SRS23470018", "SRA2029585", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-08", "Adult", "Adult", "Jaw", "Surface Structure"], [34295, "SRR31642041", "SRX27005496", "SRS23470018", "SRP550052", "PRJNA1195551", "scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint", "GSE283763", "Transcriptome Analysis", "Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.", null, null, null, "Jaw joint cells  70 dpjr  Single", "GSM8671781", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2|geo loc name:missing|collection date:missing", "Jaw joint cells  70 dpjr  Single", "CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files", "Jaw joint", "Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3\u2032 Library & Gel Bead Kit v2 10X Genomics  following the manufacturer\u2019s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.", null, "tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2", "GSM8671781", "GSM8671781: Jaw joint cells  70 dpjr  Single; Danio rerio; RNA Seq", "GSM8671781 r1", "GSM8671781", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3\u2032 Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP550052", null, "loader:fastq load.py", "70dpjr_Single_Animal_L003_I1_001.fastq.gz 70dpjr_Single_Animal_L003_I2_001.fastq.gz 70dpjr_Single_Animal_L003_R1_001.fastq.gz 70dpjr_Single_Animal_L003_R2_001.fastq.gz", "fastq fastq fastq fastq", 37422563532.0, 168570106.0, "GSM8671781 r2", "0:10 1:10 2:101 3:101", "A:9984119286;C:6706845163;G:6549173156;T:10810402697;N:621110", 10, 10, 101, 101, 9984119286, 6706845163, 6549173156, 10810402697, 621110, "SRX27005496", "SRS23470018", "SRA2029585", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-08", "Adult", "Adult", "Jaw", "Surface Structure"], [34296, "SRR31642042", "SRX27005495", "SRS23470017", "SRP550052", "PRJNA1195551", "scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint", "GSE283763", "Transcriptome Analysis", "Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.", null, null, null, "Jaw joint cells  70 dpjr  Pooled", "GSM8671780", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2|geo loc name:missing|collection date:missing", "Jaw joint cells  70 dpjr  Pooled", "CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files", "Jaw joint", "Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3\u2032 Library & Gel Bead Kit v2 10X Genomics  following the manufacturer\u2019s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.", null, "tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2", "GSM8671780", "GSM8671780: Jaw joint cells  70 dpjr  Pooled; Danio rerio; RNA Seq", "GSM8671780 r1", "GSM8671780", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3\u2032 Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP550052", null, "loader:fastq load.py", "70dpjr_Pooled_L002_I1_001.fastq.gz 70dpjr_Pooled_L002_I2_001.fastq.gz 70dpjr_Pooled_L002_R1_001.fastq.gz 70dpjr_Pooled_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 38777301438.0, 174672529.0, "GSM8671780 r1", "0:10 1:10 2:101 3:101", "A:10225368778;C:6854296513;G:6738650656;T:11464913181;N:621730", 10, 10, 101, 101, 10225368778, 6854296513, 6738650656, 11464913181, 621730, "SRX27005495", "SRS23470017", "SRA2029585", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-08", "Adult", "Adult", "Jaw", "Surface Structure"], [34297, "SRR31642043", "SRX27005495", "SRS23470017", "SRP550052", "PRJNA1195551", "scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint", "GSE283763", "Transcriptome Analysis", "Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.", null, null, null, "Jaw joint cells  70 dpjr  Pooled", "GSM8671780", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2|geo loc name:missing|collection date:missing", "Jaw joint cells  70 dpjr  Pooled", "CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files", "Jaw joint", "Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3\u2032 Library & Gel Bead Kit v2 10X Genomics  following the manufacturer\u2019s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.", null, "tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2", "GSM8671780", "GSM8671780: Jaw joint cells  70 dpjr  Pooled; Danio rerio; RNA Seq", "GSM8671780 r1", "GSM8671780", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3\u2032 Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP550052", null, "loader:fastq load.py", "70dpjr_Pooled_L003_I1_001.fastq.gz 70dpjr_Pooled_L003_I2_001.fastq.gz 70dpjr_Pooled_L003_R1_001.fastq.gz 70dpjr_Pooled_L003_R2_001.fastq.gz", "fastq fastq fastq fastq", 39504660018.0, 177948919.0, "GSM8671780 r2", "0:10 1:10 2:101 3:101", "A:10484112013;C:7025634996;G:6867358428;T:11567917628;N:658573", 10, 10, 101, 101, 10484112013, 7025634996, 6867358428, 11567917628, 658573, "SRX27005495", "SRS23470017", "SRA2029585", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-08", "Adult", "Adult", "Jaw", "Surface Structure"], [34298, "SRR31642044", "SRX27005494", "SRS23470016", "SRP550052", "PRJNA1195551", "scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint", "GSE283763", "Transcriptome Analysis", "Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.", null, null, null, "Jaw joint cells  28 dpjr  Single Animal", "GSM8671779", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2|geo loc name:missing|collection date:missing", "Jaw joint cells  28 dpjr  Single Animal", "CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files", "Jaw joint", "Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3\u2032 Library & Gel Bead Kit v2 10X Genomics  following the manufacturer\u2019s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.", null, "tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2", "GSM8671779", "GSM8671779: Jaw joint cells  28 dpjr  Single Animal; Danio rerio; RNA Seq", "GSM8671779 r1", "GSM8671779", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3\u2032 Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP550052", null, "loader:fastq load.py", "28dpjr_Single_Animal_L002_I1_001.fastq.gz 28dpjr_Single_Animal_L002_I2_001.fastq.gz 28dpjr_Single_Animal_L002_R1_001.fastq.gz 28dpjr_Single_Animal_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 36462195750.0, 164244125.0, "GSM8671779 r1", "0:10 1:10 2:101 3:101", "A:9480759740;C:6602174265;G:6480198740;T:10613598349;N:582156", 10, 10, 101, 101, 9480759740, 6602174265, 6480198740, 10613598349, 582156, "SRX27005494", "SRS23470016", "SRA2029585", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-08", "Adult", "Adult", "Jaw", "Surface Structure"], [34299, "SRR31642045", "SRX27005494", "SRS23470016", "SRP550052", "PRJNA1195551", "scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint", "GSE283763", "Transcriptome Analysis", "Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.", null, null, null, "Jaw joint cells  28 dpjr  Single Animal", "GSM8671779", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2|geo loc name:missing|collection date:missing", "Jaw joint cells  28 dpjr  Single Animal", "CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files", "Jaw joint", "Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3\u2032 Library & Gel Bead Kit v2 10X Genomics  following the manufacturer\u2019s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.", null, "tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2", "GSM8671779", "GSM8671779: Jaw joint cells  28 dpjr  Single Animal; Danio rerio; RNA Seq", "GSM8671779 r1", "GSM8671779", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3\u2032 Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP550052", null, "loader:fastq load.py", "28dpjr_Single_Animal_L003_I1_001.fastq.gz 28dpjr_Single_Animal_L003_I2_001.fastq.gz 28dpjr_Single_Animal_L003_R1_001.fastq.gz 28dpjr_Single_Animal_L003_R2_001.fastq.gz", "fastq fastq fastq fastq", 37308768774.0, 168057517.0, "GSM8671779 r2", "0:10 1:10 2:101 3:101", "A:9765937139;C:6796393106;G:6628239898;T:10756427871;N:620420", 10, 10, 101, 101, 9765937139, 6796393106, 6628239898, 10756427871, 620420, "SRX27005494", "SRS23470016", "SRA2029585", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-08", "Adult", "Adult", "Jaw", "Surface Structure"], [34300, "SRR31642046", "SRX27005493", "SRS23470015", "SRP550052", "PRJNA1195551", "scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint", "GSE283763", "Transcriptome Analysis", "Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.", null, null, null, "Jaw joint cells  28 dpjr  Pooled", "GSM8671778", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2|geo loc name:missing|collection date:missing", "Jaw joint cells  28 dpjr  Pooled", "CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files", "Jaw joint", "Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3\u2032 Library & Gel Bead Kit v2 10X Genomics  following the manufacturer\u2019s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.", null, "tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2", "GSM8671778", "GSM8671778: Jaw joint cells  28 dpjr  Pooled; Danio rerio; RNA Seq", "GSM8671778 r1", "GSM8671778", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3\u2032 Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP550052", null, "loader:fastq load.py", "28dpjr_Pooled_L002_I1_001.fastq.gz 28dpjr_Pooled_L002_I2_001.fastq.gz 28dpjr_Pooled_L002_R1_001.fastq.gz 28dpjr_Pooled_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 37406314908.0, 168496914.0, "GSM8671778 r1", "0:10 1:10 2:101 3:101", "A:9851624515;C:6742015789;G:6561704544;T:10880437218;N:594562", 10, 10, 101, 101, 9851624515, 6742015789, 6561704544, 10880437218, 594562, "SRX27005493", "SRS23470015", "SRA2029585", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-08", "Adult", "Adult", "Jaw", "Surface Structure"], [34301, "SRR31642047", "SRX27005493", "SRS23470015", "SRP550052", "PRJNA1195551", "scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint", "GSE283763", "Transcriptome Analysis", "Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.", null, null, null, "Jaw joint cells  28 dpjr  Pooled", "GSM8671778", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2|geo loc name:missing|collection date:missing", "Jaw joint cells  28 dpjr  Pooled", "CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files", "Jaw joint", "Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3\u2032 Library & Gel Bead Kit v2 10X Genomics  following the manufacturer\u2019s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.", null, "tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2", "GSM8671778", "GSM8671778: Jaw joint cells  28 dpjr  Pooled; Danio rerio; RNA Seq", "GSM8671778 r1", "GSM8671778", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. 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