{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Undetermined\" and devstage_curation_coarse = \"Adult\"", "rows": [[280, "DRR161311", "DRX151936", "DRS095335", "DRP005084", "PRJDB7735", "Gene expression profile in adult zebrafish liver", "DRP005084", "Transcriptome Analysis", "Increasing use of zebrafish in toxicological researches requires knowledge on gene expression profile in liver that play a major role in xenobiotic metabolism. Our research provide a basal gene expression profile in adult zebrafish liver.", null, null, null, "Transcriptome of female Danio rerio liver", "SAMD00153247", null, "sample name:transcriptome zebrafish female|sex:female|strain:RIKEN WT|tissue:liver", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing of SAMD00153247", "DRX151936", "f", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "NextSeq 500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP005084", "NextSeq 500 paired end sequencing of SAMD00153247", null, null, null, 2338564937.0, 15498367.0, "DRR161311", "0:75.45 1:75.44", "A:613899755;C:541756858;G:548366901;T:633083422;N:1458001", 75, 75, null, null, 613899755, 541756858, 548366901, 633083422, 1458001, "DRX151936", "DRS095335", "DRA007652", "OBICHIKU|Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine", "Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine", 2, 0.95814, 0.96362, 0.05394, 0.04517, 0.77932, 0.7834, 0.37385, 0.37264, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-05-20", "Undetermined", "Adult", "Liver", "Liver and Biliary System"], [281, "DRR161310", "DRX151935", "DRS095334", "DRP005084", "PRJDB7735", "Gene expression profile in adult zebrafish liver", "DRP005084", "Transcriptome Analysis", "Increasing use of zebrafish in toxicological researches requires knowledge on gene expression profile in liver that play a major role in xenobiotic metabolism. Our research provide a basal gene expression profile in adult zebrafish liver.", null, null, null, "Transcriptome of male Danio rerio liver", "SAMD00153246", null, "sample name:transcriptome zebrafish male|sex:male|strain:RIKEN WT|tissue:liver", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing of SAMD00153246", "DRX151935", "m", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "NextSeq 500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP005084", "NextSeq 500 paired end sequencing of SAMD00153246", null, null, null, 2506978527.0, 16611154.0, "DRR161310", "0:75.48 1:75.44", "A:672321355;C:568289588;G:569411670;T:695545626;N:1410288", 75, 75, null, null, 672321355, 568289588, 569411670, 695545626, 1410288, "DRX151935", "DRS095334", "DRA007652", "OBICHIKU|Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine", "Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine", 2, 0.94746, 0.95115, 0.07899, 0.06363, 0.80837, 0.8115, 0.52008, 0.58743, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-05-20", "Undetermined", "Adult", "Liver", "Liver and Biliary System"], [8076, "ERR2304209", "ERX2355537", "ERS2201745", "ERP106721", "PRJEB24858", "Zebrafish   modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1", "ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099", "Other", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not.", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08", null, null, "Aged mutant biorep3", "SAMEA104590463", "Adelaide Bioinformatics Hub", "ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590463|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Aged mutant biorep3|common name:zebrafish|sample name:Aged mutant biorep3", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 12", "9 psen1K97Gfshet 24mth 13 03 2014 S3 fem", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease", "Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP106721", "NextSeq 500 paired end sequencing", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16", "9_psen1K97Gfshet_24mth_13_03_2014_S3_fem_R1.fastq.gz 9_psen1K97Gfshet_24mth_13_03_2014_S3_fem_R2.fastq.gz", "fastq fastq", 9318039088.0, 38360343.0, "ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 12", "0:121.17 1:121.74", "A:2583644589;C:2091813317;G:2105322994;T:2536795040;N:463148", 121, 121, null, null, 2583644589, 2091813317, 2105322994, 2536795040, 463148, "ERX2355537", "ERS2201745", "ERA1210082", "Adelaide Bioinformatics Hub|European Nucleotide Archive", "Adelaide Bioinformatics Hub", 2, 0.93003, 0.92836, 0.26254, 0.26157, 0.68992, 0.69593, 0.48246, 0.48292, 134, 134, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2018-02-08", "Undetermined", "Adult", "Brain", "Nervous System"], [8077, "ERR2304208", "ERX2355536", "ERS2201744", "ERP106721", "PRJEB24858", "Zebrafish   modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1", "ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099", "Other", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not.", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08", null, null, "Aged mutant biorep2", "SAMEA104590462", "Adelaide Bioinformatics Hub", "ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590462|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Aged mutant biorep2|common name:zebrafish|sample name:Aged mutant biorep2", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 11", "8 psen1K97Gfshet 24mth 13 03 2014 S2 fem", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease", "Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP106721", "NextSeq 500 paired end sequencing", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16", "8_psen1K97Gfshet_24mth_13_03_2014_S2_fem_R1.fastq.gz 8_psen1K97Gfshet_24mth_13_03_2014_S2_fem_R2.fastq.gz", "fastq fastq", 8559244581.0, 35608377.0, "ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 11", "0:119.87 1:120.50", "A:2397336730;C:1892236963;G:1910506310;T:2358778868;N:385710", 119, 120, null, null, 2397336730, 1892236963, 1910506310, 2358778868, 385710, "ERX2355536", "ERS2201744", "ERA1210082", "Adelaide Bioinformatics Hub|European Nucleotide Archive", "Adelaide Bioinformatics Hub", 2, 0.92422, 0.92311, 0.30514, 0.30437, 0.69578, 0.7008, 0.49054, 0.48857, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2018-02-08", "Undetermined", "Adult", "Brain", "Nervous System"], [8078, "ERR2304207", "ERX2355535", "ERS2201743", "ERP106721", "PRJEB24858", "Zebrafish   modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1", "ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099", "Other", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not.", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08", null, null, "Aged mutant biorep1", "SAMEA104590461", "Adelaide Bioinformatics Hub", "ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590461|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Aged mutant biorep1|common name:zebrafish|sample name:Aged mutant biorep1", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 10", "7 psen1K97Gfshet 24mth 13 03 2014 S1 fem", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease", "Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP106721", "NextSeq 500 paired end sequencing", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16", "7_psen1K97Gfshet_24mth_13_03_2014_S1_fem_R1.fastq.gz 7_psen1K97Gfshet_24mth_13_03_2014_S1_fem_R2.fastq.gz", "fastq fastq", 6521711648.0, 27182062.0, "ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 10", "0:119.65 1:120.27", "A:1831722484;C:1434689482;G:1449266189;T:1805677755;N:355738", 119, 120, null, null, 1831722484, 1434689482, 1449266189, 1805677755, 355738, "ERX2355535", "ERS2201743", "ERA1210082", "Adelaide Bioinformatics Hub|European Nucleotide Archive", "Adelaide Bioinformatics Hub", 2, 0.92564, 0.92498, 0.29344, 0.29212, 0.69327, 0.69964, 0.48557, 0.48942, 86, 86, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2018-02-08", "Undetermined", "Adult", "Brain", "Nervous System"], [8079, "ERR2304206", "ERX2355534", "ERS2201742", "ERP106721", "PRJEB24858", "Zebrafish   modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1", "ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099", "Other", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not.", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08", null, null, "Aged wild type biorep3", "SAMEA104590460", "Adelaide Bioinformatics Hub", "ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590460|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Aged wild type biorep3|common name:zebrafish|sample name:Aged wild type biorep3", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 9", "3 non mutant K97Gfs 24mth 13 03 2014 S3 fem", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease", "Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP106721", "NextSeq 500 paired end sequencing", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16", "3_non_mutant_K97Gfs_24mth_13_03_2014_S3_fem_R1.fastq.gz 3_non_mutant_K97Gfs_24mth_13_03_2014_S3_fem_R2.fastq.gz", "fastq fastq", 6865452019.0, 28646225.0, "ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 9", "0:119.50 1:120.16", "A:1903309108;C:1535570672;G:1550661363;T:1875578941;N:331935", 119, 120, null, null, 1903309108, 1535570672, 1550661363, 1875578941, 331935, "ERX2355534", "ERS2201742", "ERA1210082", "Adelaide Bioinformatics Hub|European Nucleotide Archive", "Adelaide Bioinformatics Hub", 2, 0.92997, 0.92904, 0.26949, 0.26497, 0.69485, 0.70072, 0.49378, 0.50075, 96, 96, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2018-02-08", "Undetermined", "Adult", "Brain", "Nervous System"], [8080, "ERR2304205", "ERX2355533", "ERS2201741", "ERP106721", "PRJEB24858", "Zebrafish   modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1", "ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099", "Other", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not.", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08", null, null, "Aged wild type biorep2", "SAMEA104590459", "Adelaide Bioinformatics Hub", "ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590459|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Aged wild type biorep2|common name:zebrafish|sample name:Aged wild type biorep2", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 8", "2 non mutant K97Gfs 24mth 13 03 2014 S2 fem", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease", "Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP106721", "NextSeq 500 paired end sequencing", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16", "2_non_mutant_K97Gfs_24mth_13_03_2014_S2_fem_R1.fastq.gz 2_non_mutant_K97Gfs_24mth_13_03_2014_S2_fem_R2.fastq.gz", "fastq fastq", 8418868343.0, 34905186.0, "ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 8", "0:120.29 1:120.91", "A:2334515884;C:1885784857;G:1900432559;T:2297775998;N:359045", 120, 120, null, null, 2334515884, 1885784857, 1900432559, 2297775998, 359045, "ERX2355533", "ERS2201741", "ERA1210082", "Adelaide Bioinformatics Hub|European Nucleotide Archive", "Adelaide Bioinformatics Hub", 2, 0.93078, 0.92967, 0.25478, 0.25365, 0.69372, 0.69938, 0.4988, 0.49709, 132, 132, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2018-02-08", "Undetermined", "Adult", "Brain", "Nervous System"], [8081, "ERR2304204", "ERX2355532", "ERS2201740", "ERP106721", "PRJEB24858", "Zebrafish   modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1", "ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099", "Other", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not.", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08", null, null, "Aged wild type biorep1", "SAMEA104590458", "Adelaide Bioinformatics Hub", "ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590458|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Aged wild type biorep1|common name:zebrafish|sample name:Aged wild type biorep1", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 7", "1 non mutant K97Gfs 24mth 13 03 2014 S1 fem", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease", "Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP106721", "NextSeq 500 paired end sequencing", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16", "1_non_mutant_K97Gfs_24mth_13_03_2014_S1_fem_R1.fastq.gz 1_non_mutant_K97Gfs_24mth_13_03_2014_S1_fem_R2.fastq.gz", "fastq fastq", 6628468736.0, 27477727.0, "ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 7", "0:120.31 1:120.92", "A:1839014115;C:1487750495;G:1497160978;T:1804205119;N:338029", 120, 120, null, null, 1839014115, 1487750495, 1497160978, 1804205119, 338029, "ERX2355532", "ERS2201740", "ERA1210082", "Adelaide Bioinformatics Hub|European Nucleotide Archive", "Adelaide Bioinformatics Hub", 2, 0.92916, 0.92783, 0.28453, 0.28375, 0.69798, 0.70289, 0.48132, 0.48227, 125, 125, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2018-02-08", "Undetermined", "Adult", "Brain", "Nervous System"], [8082, "ERR2304203", "ERX2355531", "ERS2201739", "ERP106721", "PRJEB24858", "Zebrafish   modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1", "ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099", "Other", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not.", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08", null, null, "Young mutant biorep3", "SAMEA104590457", "Adelaide Bioinformatics Hub", "ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590457|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Young mutant biorep3|common name:zebrafish|sample name:Young mutant biorep3", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 6", "12 psen1K97Gfshet 6mth 10 03 2016 S3 fem", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease", "Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP106721", "NextSeq 500 paired end sequencing", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16", "12_psen1K97Gfshet_6mth_10_03_2016_S3_fem_R1.fastq.gz 12_psen1K97Gfshet_6mth_10_03_2016_S3_fem_R2.fastq.gz", "fastq fastq", 11485397100.0, 38284657.0, "ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 6", "0:150 1:150", "A:3206707597;C:2539306860;G:2721427816;T:3015264084;N:2690743", 150, 150, null, null, 3206707597, 2539306860, 2721427816, 3015264084, 2690743, "ERX2355531", "ERS2201739", "ERA1210082", "Adelaide Bioinformatics Hub|European Nucleotide Archive", "Adelaide Bioinformatics Hub", 2, 0.92853, 0.92813, 0.26757, 0.26433, 0.68487, 0.68903, 0.47708, 0.47074, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2018-02-08", "Undetermined", "Adult", "Brain", "Nervous System"], [8083, "ERR2304202", "ERX2355530", "ERS2201738", "ERP106721", "PRJEB24858", "Zebrafish   modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1", "ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099", "Other", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not.", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08", null, null, "Young mutant biorep2", "SAMEA104590456", "Adelaide Bioinformatics Hub", "ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590456|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Young mutant biorep2|common name:zebrafish|sample name:Young mutant biorep2", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 5", "11 psen1K97Gfshet 6mth 10 03 2016 S2 fem", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease", "Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP106721", "NextSeq 500 paired end sequencing", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16", "11_psen1K97Gfshet_6mth_10_03_2016_S2_fem_R1.fastq.gz 11_psen1K97Gfshet_6mth_10_03_2016_S2_fem_R2.fastq.gz", "fastq fastq", 13258122000.0, 44193740.0, "ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 5", "0:150 1:150", "A:3781076311;C:2868334319;G:3063279426;T:3542309854;N:3122090", 150, 150, null, null, 3781076311, 2868334319, 3063279426, 3542309854, 3122090, "ERX2355530", "ERS2201738", "ERA1210082", "Adelaide Bioinformatics Hub|European Nucleotide Archive", "Adelaide Bioinformatics Hub", 2, 0.91552, 0.91659, 0.32337, 0.32168, 0.69546, 0.698, 0.4697, 0.47295, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2018-02-08", "Undetermined", "Adult", "Brain", "Nervous System"], [8084, "ERR2304201", "ERX2355529", "ERS2201737", "ERP106721", "PRJEB24858", "Zebrafish   modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1", "ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099", "Other", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not.", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08", null, null, "Young mutant biorep1", "SAMEA104590455", "Adelaide Bioinformatics Hub", "ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590455|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Young mutant biorep1|common name:zebrafish|sample name:Young mutant biorep1", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 4", "10 psen1K97Gfshet 6mth 10 03 2016 S1 fem", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease", "Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP106721", "NextSeq 500 paired end sequencing", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16", "10_psen1K97Gfshet_6mth_10_03_2016_S1_fem_R1.fastq.gz 10_psen1K97Gfshet_6mth_10_03_2016_S1_fem_R2.fastq.gz", "fastq fastq", 11724649800.0, 39082166.0, "ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 4", "0:150 1:150", "A:3304100658;C:2560616667;G:2779636286;T:3077545106;N:2751083", 150, 150, null, null, 3304100658, 2560616667, 2779636286, 3077545106, 2751083, "ERX2355529", "ERS2201737", "ERA1210082", "Adelaide Bioinformatics Hub|European Nucleotide Archive", "Adelaide Bioinformatics Hub", 2, 0.92121, 0.91893, 0.28263, 0.27928, 0.69073, 0.6953, 0.47174, 0.46157, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2018-02-08", "Undetermined", "Adult", "Brain", "Nervous System"], [8085, "ERR2304200", "ERX2355528", "ERS2201736", "ERP106721", "PRJEB24858", "Zebrafish   modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1", "ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099", "Other", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not.", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08", null, null, "Young wild type biorep3", "SAMEA104590454", "Adelaide Bioinformatics Hub", "ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590454|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Young wild type biorep3|common name:zebrafish|sample name:Young wild type biorep3", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 3", "6 non mutant K97Gfs 6mth 10 03 2016 S3 fem", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease", "Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP106721", "NextSeq 500 paired end sequencing", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16", "6_non_mutant_K97Gfs_6mth_10_03_2016_S3_fem_R1.fastq.gz 6_non_mutant_K97Gfs_6mth_10_03_2016_S3_fem_R2.fastq.gz", "fastq fastq", 24923212200.0, 83077374.0, "ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 3", "0:150 1:150", "A:7077378299;C:5398402396;G:5838059014;T:6604505033;N:4867458", 150, 150, null, null, 7077378299, 5398402396, 5838059014, 6604505033, 4867458, "ERX2355528", "ERS2201736", "ERA1210082", "Adelaide Bioinformatics Hub|European Nucleotide Archive", "Adelaide Bioinformatics Hub", 2, 0.91973, 0.92144, 0.29148, 0.29015, 0.69587, 0.69994, 0.46145, 0.47047, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2018-02-08", "Undetermined", "Adult", "Brain", "Nervous System"], [8086, "ERR2304199", "ERX2355527", "ERS2201735", "ERP106721", "PRJEB24858", "Zebrafish   modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1", "ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099", "Other", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not.", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08", null, null, "Young wild type biorep2", "SAMEA104590453", "Adelaide Bioinformatics Hub", "ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590453|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Young wild type biorep2|common name:zebrafish|sample name:Young wild type biorep2", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 2", "5 non mutant K97Gfs 6mth 10 03 2016 S2 fem", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease", "Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP106721", "NextSeq 500 paired end sequencing", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16", "5_non_mutant_K97Gfs_6mth_10_03_2016_S2_fem_R1.fastq.gz 5_non_mutant_K97Gfs_6mth_10_03_2016_S2_fem_R2.fastq.gz", "fastq fastq", 7840317153.0, 39006553.0, "ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 2", "0:101 1:100", "A:2200490653;C:1718458832;G:1730278863;T:2188900320;N:2188485", 101, 100, null, null, 2200490653, 1718458832, 1730278863, 2188900320, 2188485, "ERX2355527", "ERS2201735", "ERA1210082", "Adelaide Bioinformatics Hub|European Nucleotide Archive", "Adelaide Bioinformatics Hub", 2, 0.91783, 0.91983, 0.32092, 0.32105, 0.67714, 0.67691, 0.47312, 0.47481, 101, 100, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2018-02-08", "Undetermined", "Adult", "Brain", "Nervous System"], [8087, "ERR2304198", "ERX2355526", "ERS2201734", "ERP106721", "PRJEB24858", "Zebrafish   modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1", "ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099", "Other", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not.", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08", null, null, "Young wild type biorep1", "SAMEA104590452", "Adelaide Bioinformatics Hub", "ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590452|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Young wild type biorep1|common name:zebrafish|sample name:Young wild type biorep1", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 1", "4 non mutant K97Gfs 6mth 10 03 2016 S1 fem", "RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease", "Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP106721", "NextSeq 500 paired end sequencing", "ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16", "4_non_mutant_K97Gfs_6mth_10_03_2016_S1_fem_R1.fastq.gz 4_non_mutant_K97Gfs_6mth_10_03_2016_S1_fem_R2.fastq.gz", "fastq fastq", 13910901600.0, 46369672.0, "ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 1", "0:150 1:150", "A:3994738757;C:2957179645;G:3191379676;T:3764325893;N:3277629", 150, 150, null, null, 3994738757, 2957179645, 3191379676, 3764325893, 3277629, "ERX2355526", "ERS2201734", "ERA1210082", "Adelaide Bioinformatics Hub|European Nucleotide Archive", "Adelaide Bioinformatics Hub", 2, 0.91399, 0.9166, 0.3202, 0.31818, 0.6942, 0.698, 0.46902, 0.47111, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2018-02-08", "Undetermined", "Adult", "Brain", "Nervous System"], [29812, "SRR27466771", "SRX23138319", "SRS20089385", "SRP482605", "PRJNA1062705", "Comparative transcriptomics coupled to developmental grading via transgenic Zebrafish reporter strains identifies conserved features in neutrophil maturation", "GSE252788", "Transcriptome Analysis", "Neutrophils are evolutionarily conserved innate immune cells playing pivotal roles in host defence. Zebrafish models have contributed substantially to our understanding of neutrophil functions but similarities to human neutrophil maturation have not been systematically characterized  which limits their applicability to studying human disease. Here we show  by generating and analysing transgenic zebrafish strains representing distinct neutrophil differentiation stages  a high resolution transcriptional profile of neutrophil maturation. We link gene expression at each stage to characteristic transcription factors  including C/ebp \u00df  which is important for late neutrophil maturation. Cross species comparison of zebrafish  mouse  and human samples confirms high molecular similarity of immature stages and discriminates zebrafish specific from pan species gene signatures. Applying the pan species neutrophil maturation signature to RNA sequencing data from human neuroblastoma patients reveals association between metastatic tumor cell infiltration in the bone marrow and an overall increase in mature neutrophils. Our detailed neutrophil maturation atlas thus provides a valuable resource for studying neutrophil function at different stages across species in health and disease. Overall design: Kidney marrow from 2 adult  six mpf  male zebrafish was isolated  labelled using lipid tagged following MULTI seq protocol  for scRNA seq using 10x Genomics.", null, "pubmed:38413586", null, "MF317 A2 GEX zebrafish multiseq", "GSM8007850", null, "source name:Kidney marrow|tissue:Kidney marrow|cell type:Whole kidney marrow PBMCs|geo loc name:missing|collection date:missing", "MF317 A2 GEX zebrafish multiseq", "We used the CellRanger v3.1.0 software 10x Genomics for cell demultiplexing and alignment and loaded the counts into Seurat v4.0.2. Assembly: GRCz11 3.1.0 zebrafish reference transcriptome that had been expanded to include the sequences of reporter genes Citrine and CFPNTR  sequences from snapgene.com. Supplementary files format and content: compressed matrix files of CellRanger outputs Supplementary files format and content: rds file containting Seurat object Supplementary files format and content: hd5a file containting Seurat object", "Kidney marrow", null, "Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 \u03bcM for 5\u2019 on ice and then incubated with lipid co anchor 2 \u03bcM for 5\u2019 on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell 3\u2019 Library & Gel Bead Kit v3.1\u202f10x Genomics  Pleasanton  CA  according to the manufacturer\u2019s protocols 10x Genomics and sequenced by protocol.", null, "tissue:Kidney marrow|cell type:Whole kidney marrow PBMCs", "GSM8007850", "GSM8007850: MF317 A2 GEX zebrafish multiseq; Danio rerio; RNA Seq", "GSM8007850 r1", "GSM8007850", "1", "Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 \u03bcM for five prime on ice and then incubated with lipid co anchor 2 \u03bcM for five prime on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell three prime Library & Gel Bead Kit v3.1\u202f10x Genomics  Pleasanton  CA  according to the manufacturer's protocols 10x Genomics and sequenced by protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP482605", null, "loader:fastq load.py", "MF317_A2_GEX_zebrafish_multiseq_S3_L004_I1_001.fastq.gz MF317_A2_GEX_zebrafish_multiseq_S3_L004_R1_001.fastq.gz MF317_A2_GEX_zebrafish_multiseq_S3_L004_R2_001.fastq.gz", "fastq fastq fastq", 20397464955.0, 151092333.0, "GSM8007850 r1", "0:8 1:29 2:98", "A:4317555978;C:3264550330;G:3319063129;T:3903632022;N:2247175", 8, 29, 98, null, 4317555978, 3264550330, 3319063129, 3903632022, 2247175, "SRX23138319", "SRS20089385", null, null, "Developmental Cancer Genomics, St. Anna Children's Cancer Research Institute (CCRI)", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Austria", "2024-01-09", "Undetermined", "Adult", "Multi-tissue", "Multi-system"], [29813, "SRR27466772", "SRX23138319", "SRS20089385", "SRP482605", "PRJNA1062705", "Comparative transcriptomics coupled to developmental grading via transgenic Zebrafish reporter strains identifies conserved features in neutrophil maturation", "GSE252788", "Transcriptome Analysis", "Neutrophils are evolutionarily conserved innate immune cells playing pivotal roles in host defence. Zebrafish models have contributed substantially to our understanding of neutrophil functions but similarities to human neutrophil maturation have not been systematically characterized  which limits their applicability to studying human disease. Here we show  by generating and analysing transgenic zebrafish strains representing distinct neutrophil differentiation stages  a high resolution transcriptional profile of neutrophil maturation. We link gene expression at each stage to characteristic transcription factors  including C/ebp \u00df  which is important for late neutrophil maturation. Cross species comparison of zebrafish  mouse  and human samples confirms high molecular similarity of immature stages and discriminates zebrafish specific from pan species gene signatures. Applying the pan species neutrophil maturation signature to RNA sequencing data from human neuroblastoma patients reveals association between metastatic tumor cell infiltration in the bone marrow and an overall increase in mature neutrophils. Our detailed neutrophil maturation atlas thus provides a valuable resource for studying neutrophil function at different stages across species in health and disease. Overall design: Kidney marrow from 2 adult  six mpf  male zebrafish was isolated  labelled using lipid tagged following MULTI seq protocol  for scRNA seq using 10x Genomics.", null, "pubmed:38413586", null, "MF317 A2 GEX zebrafish multiseq", "GSM8007850", null, "source name:Kidney marrow|tissue:Kidney marrow|cell type:Whole kidney marrow PBMCs|geo loc name:missing|collection date:missing", "MF317 A2 GEX zebrafish multiseq", "We used the CellRanger v3.1.0 software 10x Genomics for cell demultiplexing and alignment and loaded the counts into Seurat v4.0.2. Assembly: GRCz11 3.1.0 zebrafish reference transcriptome that had been expanded to include the sequences of reporter genes Citrine and CFPNTR  sequences from snapgene.com. Supplementary files format and content: compressed matrix files of CellRanger outputs Supplementary files format and content: rds file containting Seurat object Supplementary files format and content: hd5a file containting Seurat object", "Kidney marrow", null, "Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 \u03bcM for 5\u2019 on ice and then incubated with lipid co anchor 2 \u03bcM for 5\u2019 on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell 3\u2019 Library & Gel Bead Kit v3.1\u202f10x Genomics  Pleasanton  CA  according to the manufacturer\u2019s protocols 10x Genomics and sequenced by protocol.", null, "tissue:Kidney marrow|cell type:Whole kidney marrow PBMCs", "GSM8007850", "GSM8007850: MF317 A2 GEX zebrafish multiseq; Danio rerio; RNA Seq", "GSM8007850 r1", "GSM8007850", "1", "Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 \u03bcM for five prime on ice and then incubated with lipid co anchor 2 \u03bcM for five prime on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell three prime Library & Gel Bead Kit v3.1\u202f10x Genomics  Pleasanton  CA  according to the manufacturer's protocols 10x Genomics and sequenced by protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP482605", null, "loader:fastq load.py", "MF317_A2_barcode_zebrafish_multiseq_S68024_S10_L004_I1_001.fastq.gz MF317_A2_barcode_zebrafish_multiseq_S68024_S10_L004_R1_001.fastq.gz MF317_A2_barcode_zebrafish_multiseq_S68024_S10_L004_R2_001.fastq.gz", "fastq fastq fastq", 609557670.0, 4515242.0, "GSM8007850 r2", "0:8 1:29 2:98", "A:288037892;C:47138905;G:85961330;T:21289087;N:66502", 8, 29, 98, null, 288037892, 47138905, 85961330, 21289087, 66502, "SRX23138319", "SRS20089385", null, null, "Developmental Cancer Genomics, St. Anna Children's Cancer Research Institute (CCRI)", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Austria", "2024-01-09", "Undetermined", "Adult", "Multi-tissue", "Multi-system"], [29814, "SRR27466773", "SRX23138318", "SRS20089387", "SRP482605", "PRJNA1062705", "Comparative transcriptomics coupled to developmental grading via transgenic Zebrafish reporter strains identifies conserved features in neutrophil maturation", "GSE252788", "Transcriptome Analysis", "Neutrophils are evolutionarily conserved innate immune cells playing pivotal roles in host defence. Zebrafish models have contributed substantially to our understanding of neutrophil functions but similarities to human neutrophil maturation have not been systematically characterized  which limits their applicability to studying human disease. Here we show  by generating and analysing transgenic zebrafish strains representing distinct neutrophil differentiation stages  a high resolution transcriptional profile of neutrophil maturation. We link gene expression at each stage to characteristic transcription factors  including C/ebp \u00df  which is important for late neutrophil maturation. Cross species comparison of zebrafish  mouse  and human samples confirms high molecular similarity of immature stages and discriminates zebrafish specific from pan species gene signatures. Applying the pan species neutrophil maturation signature to RNA sequencing data from human neuroblastoma patients reveals association between metastatic tumor cell infiltration in the bone marrow and an overall increase in mature neutrophils. Our detailed neutrophil maturation atlas thus provides a valuable resource for studying neutrophil function at different stages across species in health and disease. Overall design: Kidney marrow from 2 adult  six mpf  male zebrafish was isolated  labelled using lipid tagged following MULTI seq protocol  for scRNA seq using 10x Genomics.", null, "pubmed:38413586", null, "MF317 A1 GEX zebrafish multiseq", "GSM8007849", null, "source name:Kidney marrow|tissue:Kidney marrow|cell type:Neutrophils|geo loc name:missing|collection date:missing", "MF317 A1 GEX zebrafish multiseq", "We used the CellRanger v3.1.0 software 10x Genomics for cell demultiplexing and alignment and loaded the counts into Seurat v4.0.2. Assembly: GRCz11 3.1.0 zebrafish reference transcriptome that had been expanded to include the sequences of reporter genes Citrine and CFPNTR  sequences from snapgene.com. Supplementary files format and content: compressed matrix files of CellRanger outputs Supplementary files format and content: rds file containting Seurat object Supplementary files format and content: hd5a file containting Seurat object", "Kidney marrow", null, "Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 \u03bcM for 5\u2019 on ice and then incubated with lipid co anchor 2 \u03bcM for 5\u2019 on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell 3\u2019 Library & Gel Bead Kit v3.1\u202f10x Genomics  Pleasanton  CA  according to the manufacturer\u2019s protocols 10x Genomics and sequenced by protocol.", null, "tissue:Kidney marrow|cell type:Neutrophils", "GSM8007849", "GSM8007849: MF317 A1 GEX zebrafish multiseq; Danio rerio; RNA Seq", "GSM8007849 r1", "GSM8007849", "1", "Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 \u03bcM for five prime on ice and then incubated with lipid co anchor 2 \u03bcM for five prime on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell three prime Library & Gel Bead Kit v3.1\u202f10x Genomics  Pleasanton  CA  according to the manufacturer's protocols 10x Genomics and sequenced by protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP482605", null, "loader:fastq load.py", "MF317_A1_GEX_zebrafish_multiseq_S1_L004_I1_001.fastq.gz MF317_A1_GEX_zebrafish_multiseq_S1_L004_R1_001.fastq.gz MF317_A1_GEX_zebrafish_multiseq_S1_L004_R2_001.fastq.gz", "fastq fastq fastq", 20471343840.0, 151639584.0, "GSM8007849 r1", "0:8 1:29 2:98", "A:4574898668;C:2902052527;G:3115258212;T:4266202403;N:2267422", 8, 29, 98, null, 4574898668, 2902052527, 3115258212, 4266202403, 2267422, "SRX23138318", "SRS20089387", null, null, "Developmental Cancer Genomics, St. Anna Children's Cancer Research Institute (CCRI)", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Austria", "2024-01-09", "Undetermined", "Adult", "Multi-tissue", "Multi-system"], [29815, "SRR27466774", "SRX23138318", "SRS20089387", "SRP482605", "PRJNA1062705", "Comparative transcriptomics coupled to developmental grading via transgenic Zebrafish reporter strains identifies conserved features in neutrophil maturation", "GSE252788", "Transcriptome Analysis", "Neutrophils are evolutionarily conserved innate immune cells playing pivotal roles in host defence. Zebrafish models have contributed substantially to our understanding of neutrophil functions but similarities to human neutrophil maturation have not been systematically characterized  which limits their applicability to studying human disease. Here we show  by generating and analysing transgenic zebrafish strains representing distinct neutrophil differentiation stages  a high resolution transcriptional profile of neutrophil maturation. We link gene expression at each stage to characteristic transcription factors  including C/ebp \u00df  which is important for late neutrophil maturation. Cross species comparison of zebrafish  mouse  and human samples confirms high molecular similarity of immature stages and discriminates zebrafish specific from pan species gene signatures. Applying the pan species neutrophil maturation signature to RNA sequencing data from human neuroblastoma patients reveals association between metastatic tumor cell infiltration in the bone marrow and an overall increase in mature neutrophils. Our detailed neutrophil maturation atlas thus provides a valuable resource for studying neutrophil function at different stages across species in health and disease. Overall design: Kidney marrow from 2 adult  six mpf  male zebrafish was isolated  labelled using lipid tagged following MULTI seq protocol  for scRNA seq using 10x Genomics.", null, "pubmed:38413586", null, "MF317 A1 GEX zebrafish multiseq", "GSM8007849", null, "source name:Kidney marrow|tissue:Kidney marrow|cell type:Neutrophils|geo loc name:missing|collection date:missing", "MF317 A1 GEX zebrafish multiseq", "We used the CellRanger v3.1.0 software 10x Genomics for cell demultiplexing and alignment and loaded the counts into Seurat v4.0.2. Assembly: GRCz11 3.1.0 zebrafish reference transcriptome that had been expanded to include the sequences of reporter genes Citrine and CFPNTR  sequences from snapgene.com. Supplementary files format and content: compressed matrix files of CellRanger outputs Supplementary files format and content: rds file containting Seurat object Supplementary files format and content: hd5a file containting Seurat object", "Kidney marrow", null, "Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 \u03bcM for 5\u2019 on ice and then incubated with lipid co anchor 2 \u03bcM for 5\u2019 on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell 3\u2019 Library & Gel Bead Kit v3.1\u202f10x Genomics  Pleasanton  CA  according to the manufacturer\u2019s protocols 10x Genomics and sequenced by protocol.", null, "tissue:Kidney marrow|cell type:Neutrophils", "GSM8007849", "GSM8007849: MF317 A1 GEX zebrafish multiseq; Danio rerio; RNA Seq", "GSM8007849 r1", "GSM8007849", "1", "Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 \u03bcM for five prime on ice and then incubated with lipid co anchor 2 \u03bcM for five prime on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell three prime Library & Gel Bead Kit v3.1\u202f10x Genomics  Pleasanton  CA  according to the manufacturer's protocols 10x Genomics and sequenced by protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP482605", null, "loader:fastq load.py", "MF317_A1_barcode_zebrafish_multiseq_S68025_S5_L004_I1_001.fastq.gz MF317_A1_barcode_zebrafish_multiseq_S68025_S5_L004_R1_001.fastq.gz MF317_A1_barcode_zebrafish_multiseq_S68025_S5_L004_R2_001.fastq.gz", "fastq fastq fastq", 205092135.0, 1519201.0, "GSM8007849 r2", "0:8 1:29 2:98", "A:96315447;C:12651302;G:31425404;T:8467378;N:22167", 8, 29, 98, null, 96315447, 12651302, 31425404, 8467378, 22167, "SRX23138318", "SRS20089387", null, null, "Developmental Cancer Genomics, St. Anna Children's Cancer Research Institute (CCRI)", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Austria", "2024-01-09", "Undetermined", "Adult", "Multi-tissue", "Multi-system"], [30512, "SRR27764782", "SRX23429747", "SRS20284188", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  cox7a1 /   replicate 4", "GSM8042779", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  cox7a1 /   replicate 4", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury", "GSM8042779", "GSM8042779: Cardiac ventricle  cox7a1 /   replicate 4; Danio rerio; RNA Seq", "GSM8042779 r1", "GSM8042779", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "KO_10_Directional_S8_R1_001.fastq.gz", "fastq", 8619450300.0, 86194503.0, "GSM8042779 r1", "0:100", "A:2183264320;C:2042597849;G:2002385828;T:2389908983;N:1293320", 100, null, null, null, 2183264320, 2042597849, 2002385828, 2389908983, 1293320, "SRX23429747", "SRS20284188", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30513, "SRR27764783", "SRX23429746", "SRS20284187", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  cox7a1 /   replicate 3", "GSM8042778", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  cox7a1 /   replicate 3", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury", "GSM8042778", "GSM8042778: Cardiac ventricle  cox7a1 /   replicate 3; Danio rerio; RNA Seq", "GSM8042778 r1", "GSM8042778", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "KO_9_Directional_S7_R1_001.fastq.gz", "fastq", 6466746100.0, 64667461.0, "GSM8042778 r1", "0:100", "A:1708351950;C:1464168743;G:1452219209;T:1841033764;N:972434", 100, null, null, null, 1708351950, 1464168743, 1452219209, 1841033764, 972434, "SRX23429746", "SRS20284187", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30514, "SRR27764784", "SRX23429745", "SRS20284186", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  cox7a1 /   replicate 2", "GSM8042777", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  cox7a1 /   replicate 2", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury", "GSM8042777", "GSM8042777: Cardiac ventricle  cox7a1 /   replicate 2; Danio rerio; RNA Seq", "GSM8042777 r1", "GSM8042777", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "KO_8_Directional_S6_R1_001.fastq.gz", "fastq", 6766795300.0, 67667953.0, "GSM8042777 r1", "0:100", "A:1803038642;C:1540664299;G:1518741633;T:1903355305;N:995421", 100, null, null, null, 1803038642, 1540664299, 1518741633, 1903355305, 995421, "SRX23429745", "SRS20284186", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30515, "SRR27764785", "SRX23429744", "SRS20284185", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  cox7a1 /   replicate 1", "GSM8042776", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  cox7a1 /   replicate 1", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury", "GSM8042776", "GSM8042776: Cardiac ventricle  cox7a1 /   replicate 1; Danio rerio; RNA Seq", "GSM8042776 r1", "GSM8042776", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "KO_7_Directional_S5_R1_001.fastq.gz", "fastq", 5583049300.0, 55830493.0, "GSM8042776 r1", "0:100", "A:1479820662;C:1265599242;G:1251078421;T:1585727832;N:823143", 100, null, null, null, 1479820662, 1265599242, 1251078421, 1585727832, 823143, "SRX23429744", "SRS20284185", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30516, "SRR27764786", "SRX23429743", "SRS20284184", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  wt sibling  replicate 4", "GSM8042775", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  wt sibling  replicate 4", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury", "GSM8042775", "GSM8042775: Cardiac ventricle  wt sibling  replicate 4; Danio rerio; RNA Seq", "GSM8042775 r1", "GSM8042775", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "WT_5_Directional_S4_R1_001.fastq.gz", "fastq", 6851217800.0, 68512178.0, "GSM8042775 r1", "0:100", "A:1837112549;C:1539284911;G:1515596368;T:1958221274;N:1002698", 100, null, null, null, 1837112549, 1539284911, 1515596368, 1958221274, 1002698, "SRX23429743", "SRS20284184", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30517, "SRR27764787", "SRX23429742", "SRS20284183", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  wt sibling  replicate 3", "GSM8042774", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  wt sibling  replicate 3", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury", "GSM8042774", "GSM8042774: Cardiac ventricle  wt sibling  replicate 3; Danio rerio; RNA Seq", "GSM8042774 r1", "GSM8042774", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "WT_3_Directional_S3_R1_001.fastq.gz", "fastq", 7036251700.0, 70362517.0, "GSM8042774 r1", "0:100", "A:1881612688;C:1574593657;G:1570342252;T:2008668471;N:1034632", 100, null, null, null, 1881612688, 1574593657, 1570342252, 2008668471, 1034632, "SRX23429742", "SRS20284183", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30518, "SRR27764788", "SRX23429741", "SRS20284182", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  wt sibling  replicate 2", "GSM8042773", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  wt sibling  replicate 2", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury", "GSM8042773", "GSM8042773: Cardiac ventricle  wt sibling  replicate 2; Danio rerio; RNA Seq", "GSM8042773 r1", "GSM8042773", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "WT_2_Directional_S2_R1_001.fastq.gz", "fastq", 6856428200.0, 68564282.0, "GSM8042773 r1", "0:100", "A:1790369167;C:1572129686;G:1566120109;T:1926782247;N:1026991", 100, null, null, null, 1790369167, 1572129686, 1566120109, 1926782247, 1026991, "SRX23429741", "SRS20284182", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30519, "SRR27764789", "SRX23429740", "SRS20284181", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  wt sibling  replicate 1", "GSM8042772", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  wt sibling  replicate 1", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury", "GSM8042772", "GSM8042772: Cardiac ventricle  wt sibling  replicate 1; Danio rerio; RNA Seq", "GSM8042772 r1", "GSM8042772", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "WT_1_Directional_S1_R1_001.fastq.gz", "fastq", 7089416800.0, 70894168.0, "GSM8042772 r1", "0:100", "A:1855346146;C:1626812736;G:1599932420;T:2006283874;N:1041624", 100, null, null, null, 1855346146, 1626812736, 1599932420, 2006283874, 1041624, "SRX23429740", "SRS20284181", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30586, "SRR27848608", "SRX23511536", "SRS20362004", "SRP487839", "PRJNA1072736", "Transgenic tools targeting striatal and pallidal subpopulations reveal both evolutionary conservation and specialization of cortico basal ganglia circuits in zebrafish", "GSE254980", "Other", "The cortico basal ganglia circuit mediates decision making. Here  we generated transgenic tools for adult zebrafish targeting specific subpopulations of the components of this circuit and utilized them to identify evolutionary homologs of the mammalian direct  and indirect pathway striatal neurons which respectively project to the homologs of the internal and external segment of the globus pallidus dEN and Vl as in mammals. Unlike in mammals  the Vl mainly projected to the dEN directly  not by way of the subthalamic nucleus. Further single cell RNA sequencing analysis revealed two pallidal output pathways: a major shortcut pathway directly connecting the dEN with the pallium and the evolutionarily conserved closed loop by way of the thalamus. Our resources and circuit map provide the common basis for the functional study of the basal ganglia in a small and optically tractable zebrafish brain for the comprehensive mechanistic understanding of the cortico basal ganglia circuit. Overall design: To identify genetic markers of the npy negative thalamus projecting neurons in the dEN  we conducted single cell RNA sequencing analysis. We dissected the dEN and its surrounding regions from six adult individuals of TgBACnpy:GAL4VP16;TgUAS:GFP. We then dissociated the dissected tissue and used the droplet based three primeend scRNAseq system Chromium 10x Genomics. We obtained transcriptomic data from 3 381 cells and performed unbiased clustering by Seurat.", null, "pubmed:38484735", null, "zebrafish dEN dissected tissue", "GSM8061694", null, "source name:dorsal entopeduncular nucleus and its surrounding brain tissue|tissue:dorsal entopeduncular nucleus and its surrounding brain tissue|cell type:Neurons/glia/blood cells from telencephalon|genotype:TgBACnpy:GAL4VP16;TgUAS:GFP|treatment:regular laboratory cultivation condition|geo loc name:missing|collection date:missing", "zebrafish dEN dissected tissue", "The obtained scRNAseq data of 3 381 cells were analyzed by Seurat.47 As a quality control  cells with more than 6% mitochondrial genes  less than 200 unique genes  and more than 17500 UMIs were removed. Barcodes with less than 500 UMIs had been already removed by cellranger count pipeline. The remaining 3 043 cells were then data normalized by LogNormalize method with scale.factor = 10000. For further calculation of UMAP and clustering  variable genes were determined with FindVariableFeatures function with selection.method = \u201cvst\u201d  and the top 2000 most highly variable genes were used for further clustering. The expression of each gene was shifted so that the mean expression across cells is 0  and scaled so that the variance across cells is 1 by ScaleData function. PCA was run on the scaled data and then UMAP and clustering were performed with the FindNeighbors function with the top 35 PCs  the FindClusters function with resolution = 0.5  and the RunUMAP function with the top 35 PCs. Dot plots and violin plots were generated by Seurat and cell types were determined by the expression of marker genes that define specific cell types. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Supplementary files format and content: HTML output file obtained from Seurat analysis using R markdown", "dorsal entopeduncular nucleus and its surrounding brain tissue", null, "Dissection was performed on 6 individuals of TgBACnpy:GAL4VP16;TgUAS:GFP fish and 12 dissected tissue pieces from the left and right hemispheres were obtained in total. The dEN and its surrounding regions were carefully dissected with micro scissors and fine forceps in ice cold and oxygenized Neurobasal medium ThermoFisher Scientific 21103049 supplemented with 1x B 27 ThermoFisher Scientific 17504044 under a fluorescent dissection microscope  as shown in the Figure S5A. The dissected tissue was dissociated with the Papain Dissociation Kit Worthington; LK003150 with 0.1% 2 mercaptoethanol for 15 minutes with gentle shaking at 28.5 degrees Celsius. Then  the cells were dissociated by gentle trituration 15 times with a glass Pasteur pipet coated with 2% BSA in PBS and spun at 300xg for 5 minutes. The cells were resuspended in papain inhibitor solution Worthington and incubated for 10 minutes with gentle shaking at 28.5 degrees Celsius. Then  the cells were further dissociated by gentle trituration 20 times with a glass Pasteur pipet attached with a regular 200 \u00b5l tip coated with 2% BSA in PBS. The dissociated cell suspension was then filtered with pluriStrainer Mini 40 \u00b5m pluriSelect coated with 2% BSA in PBS and spun at 300xg for 5 minutes. The resulting cell suspension was resuspended in 2% BSA in PBS  and then cell debris and dead cells were removed by FACS FACSAria SORP  BD Biosciences using Hoechst to sort out cells from cell debris and Propidium Iodide to sort out living cells from dead cells. post FACS sorting  a small fraction of the cell suspension was used to estimate the total number of the cells and their viability using a dead cell stain Trypan Blue elabscience. The obtained suspension contained 16 000 cells with 85.0% viability. The resulting single cell suspension was loaded on the Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1 10x Genomics  PN 1000269  and the cDNA library was prepared according to the manufacturer\u2019s instructions. The obtained cDNA library underwent Next generation sequencing by illumina Hiseq X GENEWIZ with 400 429 716 total reads and 85.9% of sequencing saturation. The obtained sequence was then analyzed by \u201cCell Ranger count\u201d pipeline provided by 10x Genomics with default options. The reads were aligned to zebrafish reference transcriptome ENSEMBL Zv11  release 99 and EGFP CDS  which were built by \u201cCell Ranger mkref\u201d command based on zebrafish reference genome GRCz11 and annotation Ensembl 99. This resulted in 3 381 estimated number of cells with 4890 median unique molecular identifier UMI counts per cell.", "regular laboratory cultivation condition", "tissue:dorsal entopeduncular nucleus and its surrounding brain tissue|cell type:Neurons/glia/blood cells from telencephalon|genotype:TgBACnpy:GAL4VP16;TgUAS:GFP|treatment:regular laboratory cultivation condition", "GSM8061694", "GSM8061694: zebrafish dEN dissected tissue; Danio rerio; RNA Seq", "GSM8061694 r1", "GSM8061694", "1", "Dissection was performed on 6 individuals of TgBACnpy:GAL4VP16;TgUAS:GFP fish and 12 dissected tissue pieces from the left and right hemispheres were obtained in total. The dEN and its surrounding regions were carefully dissected with micro scissors and fine forceps in ice cold and oxygenized Neurobasal medium ThermoFisher Scientific 21103049 supplemented with 1x B 27 ThermoFisher Scientific 17504044 under a fluorescent dissection microscope  as shown in the Figure S5A. The dissected tissue was dissociated with the Papain Dissociation Kit Worthington; LK003150 with 0.1% 2 mercaptoethanol for 15 minutes with gentle shaking at 28.5 degrees Celsius. Then  the cells were dissociated by gentle trituration 15 times with a glass Pasteur pipet coated with 2% BSA in PBS and spun at 300xg for 5 minutes. The cells were resuspended in papain inhibitor solution Worthington and incubated for 10 minutes with gentle shaking at 28.5 degrees Celsius. Then  the cells were further dissociated by gentle trituration 20 times with a glass Pasteur pipet attached with a regular 200 \u00b5l tip coated with 2% BSA in PBS. The dissociated cell suspension was then filtered with pluriStrainer Mini 40 \u00b5m pluriSelect coated with 2% BSA in PBS and spun at 300xg for 5 minutes. The resulting cell suspension was resuspended in 2% BSA in PBS  and then cell debris and dead cells were removed by FACS FACSAria SORP  BD Biosciences using Hoechst to sort out cells from cell debris and Propidium Iodide to sort out living cells from dead cells. post FACS sorting  a small fraction of the cell suspension was used to estimate the total number of the cells and their viability using a dead cell stain Trypan Blue elabscience. The obtained suspension contained 16 000 cells with 85.0% viability. The resulting single cell suspension was loaded on the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 10x Genomics  PN 1000269  and the cDNA library was prepared according to the manufacturer's instructions. The obtained cDNA library underwent Next generation sequencing by illumina Hiseq X GENEWIZ with 400 429 716 total reads and 85.9% of sequencing saturation. The obtained sequence was then analyzed by \u201cCell Ranger count\u201d pipeline provided by 10x Genomics with default options. The reads were aligned to zebrafish reference transcriptome ENSEMBL Zv11  release 99 and EGFP CDS  which were built by \u201cCell Ranger mkref\u201d command based on zebrafish reference genome GRCz11 and annotation Ensembl 99. This resulted in 3 381 estimated number of cells with 4890 median unique molecular identifier UMI counts per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP487839", null, "loader:fastq load.py", "ENcDNALibrary20210701_S1_L002_I1_001.fastq.gz ENcDNALibrary20210701_S1_L002_I2_001.fastq.gz ENcDNALibrary20210701_S1_L002_R1_001.fastq.gz ENcDNALibrary20210701_S1_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 53657581944.0, 400429716.0, "GSM8061694 r1", "0:8 1:8 2:28 3:90", "A:10793191703;C:7078696830;G:7719702279;T:10444591093;N:2492535", 8, 8, 28, 90, 10793191703, 7078696830, 7719702279, 10444591093, 2492535, "SRX23511536", "SRS20362004", "SRA1796958", "CBS, RIKEN", "CBS, RIKEN", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Japan", "2024-02-02", "Undetermined", "Adult", "Brain", "Nervous System"], [30746, "SRR28348607", "SRX23954674", "SRS20755104", "SRP495302", "PRJNA1088122", "Decoding the molecular  cellular  and functional heterogeneity of zebrafish intracardiac nervous system", "GSE261619", "Transcriptome Analysis", "In this project  we present a comprehensive taxonomy of the intracardiac nervous system IcNS  utilizing single cell RNA sequencing  anatomical studies  and electrophysiological techniques. Overall design: For single cell sequencing experiments  25 Tgelavl3:eGFP previously known as HuC:GFP of 5 mpf animal were used from both sexes for the first set and 25 Tgelavl3:eGFP of 11 mpf  and 10 Tgnbt:DsRed of 22 mpf animals from both sexes were used for the second set. Cells were dissociated sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation and cDNA synthesis done by following 10X Genomics' workflows. The reads were aligned to zebrafish genome GRChZ 11  v 105 was used for gene annotation and assigning reads to genes. Cellranger software version 6.1.2 was used to process the data.", null, "pubmed:39632839", null, "Tgelavl3:eGFP  Tgnbt:DsRed", "GSM8147512", null, "source name:atrium|tissue:atrium|genotype:Tgelavl3:eGFP  Tgnbt:DsRed|geo loc name:missing|collection date:missing", "Tgelavl3:eGFP  Tgnbt:DsRed", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genomics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger", "atrium", null, "Cells from zebrafish heart were dissociated. In addition to GFP and DsRed in the genome of the fish  viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics", "Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH7.5  at 28\u00b0C \u00b11\u00b0C in groups of 20 animals per 2.8L.", "tissue:atrium|genotype:Tgelavl3:eGFP  Tgnbt:DsRed", "GSM8147512", "GSM8147512: Tgelavl3:eGFP  Tgnbt:DsRed; Danio rerio; RNA Seq", "GSM8147512 r1", "GSM8147512", "1", "Cells from zebrafish heart were dissociated. In addition to GFP and DsRed in the genome of the fish  viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP495302", null, "loader:fastq load.py", "CP030_S1_L004_I1_001.fastq.gz CP030_S1_L004_I2_001.fastq.gz CP030_S1_L004_R1_001.fastq.gz CP030_S1_L004_R2_001.fastq.gz", "fastq fastq fastq fastq", 86914563102.0, 391507041.0, "GSM8147512 r1", "0:10 1:10 2:101 3:101", "A:23707102309;C:15625825731;G:14915197158;T:24834868356;N:1428728", 10, 10, 101, 101, 23707102309, 15625825731, 14915197158, 24834868356, 1428728, "SRX23954674", "SRS20755104", "SRA1824602", "Neurology &amp; TAUB Institute, Columbia University", "Neurology & TAUB Institute, Columbia University", 2, 0.0, 0.94374, 0.0, 0.12308, 1.0, 0.82055, null, 0.55544, 101, 101, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-03-14", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30747, "SRR28348608", "SRX23954673", "SRS20755103", "SRP495302", "PRJNA1088122", "Decoding the molecular  cellular  and functional heterogeneity of zebrafish intracardiac nervous system", "GSE261619", "Transcriptome Analysis", "In this project  we present a comprehensive taxonomy of the intracardiac nervous system IcNS  utilizing single cell RNA sequencing  anatomical studies  and electrophysiological techniques. Overall design: For single cell sequencing experiments  25 Tgelavl3:eGFP previously known as HuC:GFP of 5 mpf animal were used from both sexes for the first set and 25 Tgelavl3:eGFP of 11 mpf  and 10 Tgnbt:DsRed of 22 mpf animals from both sexes were used for the second set. Cells were dissociated sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation and cDNA synthesis done by following 10X Genomics' workflows. The reads were aligned to zebrafish genome GRChZ 11  v 105 was used for gene annotation and assigning reads to genes. Cellranger software version 6.1.2 was used to process the data.", null, "pubmed:39632839", null, "Tgelavl3:eGFP", "GSM8147511", null, "source name:whole heart|tissue:whole heart|genotype:Tgelavl3:eGFP|geo loc name:missing|collection date:missing", "Tgelavl3:eGFP", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genomics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger", "whole heart", null, "Cells from zebrafish heart were dissociated. In addition to GFP and DsRed in the genome of the fish  viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics", "Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH7.5  at 28\u00b0C \u00b11\u00b0C in groups of 20 animals per 2.8L.", "tissue:whole heart|genotype:Tgelavl3:eGFP", "GSM8147511", "GSM8147511: Tgelavl3:eGFP; Danio rerio; RNA Seq", "GSM8147511 r1", "GSM8147511", "1", "Cells from zebrafish heart were dissociated. In addition to GFP and DsRed in the genome of the fish  viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP495302", null, "loader:fastq load.py", "CP017_S1_L001_I1_001.fastq.gz CP017_S1_L001_I2_001.fastq.gz CP017_S1_L001_R1_001.fastq.gz CP017_S1_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 41176621272.0, 185480276.0, "GSM8147511 r1", "0:10 1:10 2:101 3:101", "A:9993088511;C:6520920913;G:6513822557;T:14438876590;N:307181", 10, 10, 101, 101, 9993088511, 6520920913, 6513822557, 14438876590, 307181, "SRX23954673", "SRS20755103", "SRA1824602", "Neurology &amp; TAUB Institute, Columbia University", "Neurology & TAUB Institute, Columbia University", 2, 0.01251, 0.96696, 0.0018, 0.07994, 0.9922, 0.83861, 0.46366, 0.47886, 101, 101, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-03-14", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30748, "SRR28348609", "SRX23954673", "SRS20755103", "SRP495302", "PRJNA1088122", "Decoding the molecular  cellular  and functional heterogeneity of zebrafish intracardiac nervous system", "GSE261619", "Transcriptome Analysis", "In this project  we present a comprehensive taxonomy of the intracardiac nervous system IcNS  utilizing single cell RNA sequencing  anatomical studies  and electrophysiological techniques. Overall design: For single cell sequencing experiments  25 Tgelavl3:eGFP previously known as HuC:GFP of 5 mpf animal were used from both sexes for the first set and 25 Tgelavl3:eGFP of 11 mpf  and 10 Tgnbt:DsRed of 22 mpf animals from both sexes were used for the second set. Cells were dissociated sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation and cDNA synthesis done by following 10X Genomics' workflows. The reads were aligned to zebrafish genome GRChZ 11  v 105 was used for gene annotation and assigning reads to genes. Cellranger software version 6.1.2 was used to process the data.", null, "pubmed:39632839", null, "Tgelavl3:eGFP", "GSM8147511", null, "source name:whole heart|tissue:whole heart|genotype:Tgelavl3:eGFP|geo loc name:missing|collection date:missing", "Tgelavl3:eGFP", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genomics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger", "whole heart", null, "Cells from zebrafish heart were dissociated. In addition to GFP and DsRed in the genome of the fish  viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics", "Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH7.5  at 28\u00b0C \u00b11\u00b0C in groups of 20 animals per 2.8L.", "tissue:whole heart|genotype:Tgelavl3:eGFP", "GSM8147511", "GSM8147511: Tgelavl3:eGFP; Danio rerio; RNA Seq", "GSM8147511 r1", "GSM8147511", "1", "Cells from zebrafish heart were dissociated. In addition to GFP and DsRed in the genome of the fish  viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP495302", null, "loader:fastq load.py", "CP017_S1_L002_I1_001.fastq.gz CP017_S1_L002_I2_001.fastq.gz CP017_S1_L002_R1_001.fastq.gz CP017_S1_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 41449667730.0, 186710215.0, "GSM8147511 r2", "0:10 1:10 2:101 3:101", "A:10111586707;C:6536521889;G:6498472573;T:14568538148;N:344113", 10, 10, 101, 101, 10111586707, 6536521889, 6498472573, 14568538148, 344113, "SRX23954673", "SRS20755103", "SRA1824602", "Neurology &amp; TAUB Institute, Columbia University", "Neurology & TAUB Institute, Columbia University", 2, 0.01136, 0.96721, 0.00127, 0.07919, 0.99299, 0.83956, 0.4846, 0.4789, 101, 101, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-03-14", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [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", "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"], [34171, "SRR31377610", "SRX26751139", "SRS23239753", "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 4", "GSM8636991", null, "source name:whole brain|tissue:whole brain|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing", "CCSER1 S 4", "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 brain", 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 brain|genotype:CCSER1 S48Y*", "GSM8636991", "GSM8636991: CCSER1 S 4; Danio rerio; RNA Seq", "GSM8636991 r1", "GSM8636991", "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, "RZW023_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW023_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 4549522488.0, 15064644.0, "GSM8636991 r1", "0:151 1:151", "A:1250060197;C:1021532178;G:1043498294;T:1233983164;N:448655", 151, 151, null, null, 1250060197, 1021532178, 1043498294, 1233983164, 448655, "SRX26751139", "SRS23239753", "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", "Brain", "Nervous System"], [34172, "SRR31377611", "SRX26751138", "SRS23239750", "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 3", "GSM8636990", null, "source name:whole brain|tissue:whole brain|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing", "CCSER1 S 3", "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 brain", 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 brain|genotype:CCSER1 S48Y*", "GSM8636990", "GSM8636990: CCSER1 S 3; Danio rerio; RNA Seq", "GSM8636990 r1", "GSM8636990", "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, "RZW022_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW022_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 4037745738.0, 13370019.0, "GSM8636990 r1", "0:151 1:151", "A:1115788839;C:903089369;G:919668882;T:1098805166;N:393482", 151, 151, null, null, 1115788839, 903089369, 919668882, 1098805166, 393482, "SRX26751138", "SRS23239750", "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", "Brain", "Nervous System"], [34173, "SRR31377612", "SRX26751137", "SRS23239751", "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 2", "GSM8636989", null, "source name:whole brain|tissue:whole brain|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing", "CCSER1 S 2", "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 brain", 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 brain|genotype:CCSER1 S48Y*", "GSM8636989", "GSM8636989: CCSER1 S 2; Danio rerio; RNA Seq", "GSM8636989 r1", "GSM8636989", "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, "RZW021_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW021_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 4443862654.0, 14714777.0, "GSM8636989 r1", "0:151 1:151", "A:1224395598;C:997142613;G:1015338597;T:1206548055;N:437791", 151, 151, null, null, 1224395598, 997142613, 1015338597, 1206548055, 437791, "SRX26751137", "SRS23239751", "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", "Brain", "Nervous System"], [34174, "SRR31377613", "SRX26751136", "SRS23239749", "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 1", "GSM8636988", null, "source name:whole brain|tissue:whole brain|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing", "CCSER1 S 1", "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 brain", 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 brain|genotype:CCSER1 S48Y*", "GSM8636988", "GSM8636988: CCSER1 S 1; Danio rerio; RNA Seq", "GSM8636988 r1", "GSM8636988", "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, "RZW020_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW020_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 3872377484.0, 12822442.0, "GSM8636988 r1", "0:151 1:151", "A:1078340804;C:859480661;G:877860528;T:1056319960;N:375531", 151, 151, null, null, 1078340804, 859480661, 877860528, 1056319960, 375531, "SRX26751136", "SRS23239749", "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", "Brain", "Nervous System"], [34175, "SRR31377614", "SRX26751135", "SRS23239748", "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 4", "GSM8636987", null, "source name:whole brain|tissue:whole brain|genotype:CCSER1 P471|geo loc name:missing|collection date:missing", "CCSER1 M 4", "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 brain", 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 brain|genotype:CCSER1 P471", "GSM8636987", "GSM8636987: CCSER1 M 4; Danio rerio; RNA Seq", "GSM8636987 r1", "GSM8636987", "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, "RZW019_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW019_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 4351542764.0, 14409082.0, "GSM8636987 r1", "0:151 1:151", "A:1201754674;C:971267214;G:998493816;T:1179600053;N:427007", 151, 151, null, null, 1201754674, 971267214, 998493816, 1179600053, 427007, "SRX26751135", "SRS23239748", "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", "Brain", "Nervous System"], [34176, "SRR31377615", "SRX26751134", "SRS23239746", "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 3", "GSM8636986", null, "source name:whole brain|tissue:whole brain|genotype:CCSER1 P471|geo loc name:missing|collection date:missing", "CCSER1 M 3", "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 brain", 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 brain|genotype:CCSER1 P471", "GSM8636986", "GSM8636986: CCSER1 M 3; Danio rerio; RNA Seq", "GSM8636986 r1", "GSM8636986", "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, "RZW018_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW018_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 3545215146.0, 11739123.0, "GSM8636986 r1", "0:151 1:151", "A:979072184;C:795835642;G:808440016;T:961524650;N:342654", 151, 151, null, null, 979072184, 795835642, 808440016, 961524650, 342654, "SRX26751134", "SRS23239746", "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", "Brain", "Nervous System"], [34177, "SRR31377616", "SRX26751133", "SRS23239747", "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 2", "GSM8636985", null, "source name:whole brain|tissue:whole brain|genotype:CCSER1 P471|geo loc name:missing|collection date:missing", "CCSER1 M 2", "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 brain", 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 brain|genotype:CCSER1 P471", "GSM8636985", "GSM8636985: CCSER1 M 2; Danio rerio; RNA Seq", "GSM8636985 r1", "GSM8636985", "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, "RZW017_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW017_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 4397314488.0, 14560644.0, "GSM8636985 r1", "0:151 1:151", "A:1212053871;C:984983253;G:1007152300;T:1192699120;N:425944", 151, 151, null, null, 1212053871, 984983253, 1007152300, 1192699120, 425944, "SRX26751133", "SRS23239747", "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", "Brain", "Nervous System"], [34178, "SRR31377617", "SRX26751132", "SRS23239745", "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 1", "GSM8636984", null, "source name:whole brain|tissue:whole brain|genotype:CCSER1 P471|geo loc name:missing|collection date:missing", "CCSER1 M 1", "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 brain", 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 brain|genotype:CCSER1 P471", "GSM8636984", "GSM8636984: CCSER1 M 1; Danio rerio; RNA Seq", "GSM8636984 r1", "GSM8636984", "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, "RZW016_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW016_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 3893147534.0, 12891217.0, "GSM8636984 r1", "0:151 1:151", "A:1070551112;C:876532821;G:895610992;T:1050076103;N:376506", 151, 151, null, null, 1070551112, 876532821, 895610992, 1050076103, 376506, "SRX26751132", "SRS23239745", "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", "Brain", "Nervous System"], [34179, "SRR31377618", "SRX26751131", "SRS23239743", "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 3.", "GSM8636983", null, "source name:whole brain|tissue:whole brain|genotype:WT|geo loc name:missing|collection date:missing", "WT 3.", "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 brain", 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 brain|genotype:WT", "GSM8636983", "GSM8636983: WT 3.; Danio rerio; RNA Seq", "GSM8636983 r1", "GSM8636983", "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, "RZW015_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW015_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 4136426956.0, 13696778.0, "GSM8636983 r1", "0:151 1:151", "A:1154437871;C:913451691;G:936555072;T:1131573396;N:408926", 151, 151, null, null, 1154437871, 913451691, 936555072, 1131573396, 408926, "SRX26751131", "SRS23239743", "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", "Brain", "Nervous System"], [34180, "SRR31377619", "SRX26751130", "SRS23239744", "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 2.", "GSM8636982", null, "source name:whole brain|tissue:whole brain|genotype:WT|geo loc name:missing|collection date:missing", "WT 2.", "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 brain", 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 brain|genotype:WT", "GSM8636982", "GSM8636982: WT 2.; Danio rerio; RNA Seq", "GSM8636982 r1", "GSM8636982", "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, "RZW014_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW014_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 3725517300.0, 12336150.0, "GSM8636982 r1", "0:151 1:151", "A:1029563963;C:833698018;G:851128447;T:1010762356;N:364516", 151, 151, null, null, 1029563963, 833698018, 851128447, 1010762356, 364516, "SRX26751130", "SRS23239744", "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", "Brain", "Nervous System"], [34181, "SRR31377620", "SRX26751129", "SRS23239742", "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 1.", "GSM8636981", null, "source name:whole brain|tissue:whole brain|genotype:WT|geo loc name:missing|collection date:missing", "WT 1.", "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 brain", 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 brain|genotype:WT", "GSM8636981", "GSM8636981: WT 1.; Danio rerio; RNA Seq", "GSM8636981 r1", "GSM8636981", "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, "RZW013_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW013_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz", "fastq fastq", 3675466840.0, 12170420.0, "GSM8636981 r1", "0:151 1:151", "A:1024674488;C:812714996;G:831919969;T:1005797546;N:359841", 151, 151, null, null, 1024674488, 812714996, 831919969, 1005797546, 359841, "SRX26751129", "SRS23239742", "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", "Brain", "Nervous System"], [34593, "SRR32128857", "SRX27475161", "SRS23899211", "SRP559934", "PRJNA1215774", "3 mpf dark reared zebrafish eye RNA sequencing", "PRJNA1215774", "Other", "Outdoor time and light intensity are important emerging factors affecting myopia; however  the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment  3 mpf zebrafish eye RNA sequencing was performed.", null, null, null, null, "lighttreated4", null, "strain:not applicable|isolate:Sun Yat sen University|breed:not applicable10|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable10|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish10|isolation source:zebrafish10|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample info", "library 10", "library 10", "DNA barcode10", null, null, "WXS", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP559934", null, null, "lighttreated4.read1.fastq.gz lighttreated4.read2.fastq.gz", "fastq fastq", 6388100400.0, 21293668.0, "lighttreated4.read1.fastq.gz", "0:150 1:150", "A:1711345062;C:1474552325;G:1531680528;T:1670485285;N:37200", 150, 150, null, null, 1711345062, 1474552325, 1531680528, 1670485285, 37200, "SRX27475161", "SRS23899211", "SRA2060897", "zhujiang hospital|ophthalmology", "zhujiang hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-25", "Undetermined", "Adult", "Undetermined", "Undetermined"], [34594, "SRR32128858", "SRX27475160", "SRS23899210", "SRP559934", "PRJNA1215774", "3 mpf dark reared zebrafish eye RNA sequencing", "PRJNA1215774", "Other", "Outdoor time and light intensity are important emerging factors affecting myopia; however  the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment  3 mpf zebrafish eye RNA sequencing was performed.", null, null, null, null, "lighttreated3", null, "strain:not applicable|isolate:Sun Yat sen University|breed:not applicable9|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable9|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish9|isolation source:zebrafish9|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample info", "library 9", "library 9", "DNA barcode9", null, null, "WXS", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP559934", null, null, "lighttreated3.read1.fastq.gz lighttreated3.read2.fastq.gz", "fastq fastq", 7919383200.0, 26397944.0, "lighttreated3.read1.fastq.gz", "0:150 1:150", "A:2135212601;C:1813586654;G:1892878979;T:2077658764;N:46202", 150, 150, null, null, 2135212601, 1813586654, 1892878979, 2077658764, 46202, "SRX27475160", "SRS23899210", "SRA2060897", "zhujiang hospital|ophthalmology", "zhujiang hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-25", "Undetermined", "Adult", "Undetermined", "Undetermined"], [34595, "SRR32128859", "SRX27475159", "SRS23899209", "SRP559934", "PRJNA1215774", "3 mpf dark reared zebrafish eye RNA sequencing", "PRJNA1215774", "Other", "Outdoor time and light intensity are important emerging factors affecting myopia; however  the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment  3 mpf zebrafish eye RNA sequencing was performed.", null, null, null, null, "lighttreated2", null, "strain:not applicable|isolate:Sun Yat sen University|breed:not applicable8|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable8|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish8|isolation source:zebrafish8|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample info", "library 8", "library 8", "DNA barcode8", null, null, "WXS", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP559934", null, null, "lighttreated2.read1.fastq.gz lighttreated2.read2.fastq.gz", "fastq fastq", 7060994100.0, 23536647.0, "lighttreated2.read1.fastq.gz", "0:150 1:150", "A:1921099545;C:1595276449;G:1668657714;T:1875918159;N:42233", 150, 150, null, null, 1921099545, 1595276449, 1668657714, 1875918159, 42233, "SRX27475159", "SRS23899209", "SRA2060897", "zhujiang hospital|ophthalmology", "zhujiang hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-25", "Undetermined", "Adult", "Undetermined", "Undetermined"], [34596, "SRR32128860", "SRX27475158", "SRS23899208", "SRP559934", "PRJNA1215774", "3 mpf dark reared zebrafish eye RNA sequencing", "PRJNA1215774", "Other", "Outdoor time and light intensity are important emerging factors affecting myopia; however  the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment  3 mpf zebrafish eye RNA sequencing was performed.", null, null, null, null, "lighttreated1", null, "strain:not applicable|isolate:Sun Yat sen University|breed:not applicable7|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable7|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish7|isolation source:zebrafish7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample info", "library 7", "library 7", "DNA barcode7", null, null, "WXS", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP559934", null, null, "lighttreated1.read1.fastq.gz lighttreated1.read2.fastq.gz", "fastq fastq", 6908625300.0, 23028751.0, "lighttreated1.read1.fastq.gz", "0:150 1:150", "A:1872190225;C:1565342714;G:1644929113;T:1826124355;N:38893", 150, 150, null, null, 1872190225, 1565342714, 1644929113, 1826124355, 38893, "SRX27475158", "SRS23899208", "SRA2060897", "zhujiang hospital|ophthalmology", "zhujiang hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-25", "Undetermined", "Adult", "Undetermined", "Undetermined"], [34597, "SRR32128861", "SRX27475157", "SRS23899207", "SRP559934", "PRJNA1215774", "3 mpf dark reared zebrafish eye RNA sequencing", "PRJNA1215774", "Other", "Outdoor time and light intensity are important emerging factors affecting myopia; however  the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment  3 mpf zebrafish eye RNA sequencing was performed.", null, null, null, null, "darktreated6", null, "strain:not applicable|isolate:Sun Yat sen University|breed:not applicable6|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable6|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish6|isolation source:zebrafish6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample info", "library 6", "library 6", "DNA barcode6", null, null, "WXS", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP559934", null, null, "darktreated6.read1.fastq.gz darktreated6.read2.fastq.gz", "fastq fastq", 8601630900.0, 28672103.0, "darktreated6.read1.fastq.gz", "0:150 1:150", "A:2318530970;C:1973292572;G:2040962638;T:2268796005;N:48715", 150, 150, null, null, 2318530970, 1973292572, 2040962638, 2268796005, 48715, "SRX27475157", "SRS23899207", "SRA2060897", "zhujiang hospital|ophthalmology", "zhujiang hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-25", "Undetermined", "Adult", "Undetermined", "Undetermined"], [34598, "SRR32128862", "SRX27475156", "SRS23899206", "SRP559934", "PRJNA1215774", "3 mpf dark reared zebrafish eye RNA sequencing", "PRJNA1215774", "Other", "Outdoor time and light intensity are important emerging factors affecting myopia; however  the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment  3 mpf zebrafish eye RNA sequencing was performed.", null, null, null, null, "darktreated5", null, "strain:not applicable|isolate:Sun Yat sen University|breed:not applicable5|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable5|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish5|isolation source:zebrafish5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample info", "library 5", "library 5", "DNA barcode5", null, null, "WXS", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP559934", null, null, "darktreated5.read1.fastq.gz darktreated5.read2.fastq.gz", "fastq fastq", 8265255300.0, 27550851.0, "darktreated5.read1.fastq.gz", "0:150 1:150", "A:2224219375;C:1898065838;G:1969603341;T:2173318912;N:47834", 150, 150, null, null, 2224219375, 1898065838, 1969603341, 2173318912, 47834, "SRX27475156", "SRS23899206", "SRA2060897", "zhujiang hospital|ophthalmology", "zhujiang hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-25", "Undetermined", "Adult", "Undetermined", "Undetermined"], [34599, "SRR32128863", "SRX27475155", "SRS23899205", "SRP559934", "PRJNA1215774", "3 mpf dark reared zebrafish eye RNA sequencing", "PRJNA1215774", "Other", "Outdoor time and light intensity are important emerging factors affecting myopia; however  the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment  3 mpf zebrafish eye RNA sequencing was performed.", null, null, null, null, "darktreated4", null, "strain:not applicable|isolate:Sun Yat sen University|breed:not applicable4|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable4|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish4|isolation source:zebrafish4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample info", "library 4", "library 4", "DNA barcode4", null, null, "WXS", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP559934", null, null, "darktreated4.read1.fastq.gz darktreated4.read2.fastq.gz", "fastq fastq", 8061663600.0, 26872212.0, "darktreated4.read1.fastq.gz", "0:150 1:150", "A:2171664867;C:1853256385;G:1909447014;T:2127248788;N:46546", 150, 150, null, null, 2171664867, 1853256385, 1909447014, 2127248788, 46546, "SRX27475155", "SRS23899205", "SRA2060897", "zhujiang hospital|ophthalmology", "zhujiang hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-25", "Undetermined", "Adult", "Undetermined", "Undetermined"], [34600, "SRR32128864", "SRX27475154", "SRS23899204", "SRP559934", "PRJNA1215774", "3 mpf dark reared zebrafish eye RNA sequencing", "PRJNA1215774", "Other", "Outdoor time and light intensity are important emerging factors affecting myopia; however  the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment  3 mpf zebrafish eye RNA sequencing was performed.", null, null, null, null, "darktreated3", null, "strain:not applicable|isolate:Sun Yat sen University|breed:not applicable3|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable3|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish3|isolation source:zebrafish3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample info", "library 3", "library 3", "DNA barcode3", null, null, "WXS", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP559934", null, null, "darktreated3.read1.fastq.gz darktreated3.read2.fastq.gz", "fastq fastq", 8287650300.0, 27625501.0, "darktreated3.read1.fastq.gz", "0:150 1:150", "A:2231337901;C:1902488349;G:1971440974;T:2182335741;N:47335", 150, 150, null, null, 2231337901, 1902488349, 1971440974, 2182335741, 47335, "SRX27475154", "SRS23899204", "SRA2060897", "zhujiang hospital|ophthalmology", "zhujiang hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-25", "Undetermined", "Adult", "Undetermined", "Undetermined"], [34601, "SRR32128865", "SRX27475153", "SRS23899203", "SRP559934", "PRJNA1215774", "3 mpf dark reared zebrafish eye RNA sequencing", "PRJNA1215774", "Other", "Outdoor time and light intensity are important emerging factors affecting myopia; however  the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment  3 mpf zebrafish eye RNA sequencing was performed.", null, null, null, null, "lighttreated6", null, "strain:not applicable|isolate:Sun Yat sen University|breed:not applicable12|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable12|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish12|isolation source:zebrafish12|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample info", "library 12", "library 12", "DNA barcode12", null, null, "WXS", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP559934", null, null, "lighttreated6.read1.fastq.gz lighttreated6.read2.fastq.gz", "fastq fastq", 7610579400.0, 25368598.0, "lighttreated6.read1.fastq.gz", "0:150 1:150", "A:2063115765;C:1733106391;G:1795336188;T:2018975316;N:45740", 150, 150, null, null, 2063115765, 1733106391, 1795336188, 2018975316, 45740, "SRX27475153", "SRS23899203", "SRA2060897", "zhujiang hospital|ophthalmology", "zhujiang hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-25", "Undetermined", "Adult", "Undetermined", "Undetermined"], [34602, "SRR32128866", "SRX27475152", "SRS23899202", "SRP559934", "PRJNA1215774", "3 mpf dark reared zebrafish eye RNA sequencing", "PRJNA1215774", "Other", "Outdoor time and light intensity are important emerging factors affecting myopia; however  the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment  3 mpf zebrafish eye RNA sequencing was performed.", null, null, null, null, "lighttreated5", null, "strain:not applicable|isolate:Sun Yat sen University|breed:not applicable11|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable11|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish11|isolation source:zebrafish11|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample info", "library 11", "library 11", "DNA barcode11", null, null, "WXS", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP559934", null, null, "lighttreated5.read1.fastq.gz lighttreated5.read2.fastq.gz", "fastq fastq", 6677234100.0, 22257447.0, "lighttreated5.read1.fastq.gz", "0:150 1:150", "A:1812295746;C:1506030273;G:1585674870;T:1773195250;N:37961", 150, 150, null, null, 1812295746, 1506030273, 1585674870, 1773195250, 37961, "SRX27475152", "SRS23899202", "SRA2060897", "zhujiang hospital|ophthalmology", "zhujiang hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-25", "Undetermined", "Adult", "Undetermined", "Undetermined"], [34603, "SRR32128867", "SRX27475151", "SRS23899201", "SRP559934", "PRJNA1215774", "3 mpf dark reared zebrafish eye RNA sequencing", "PRJNA1215774", "Other", "Outdoor time and light intensity are important emerging factors affecting myopia; however  the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment  3 mpf zebrafish eye RNA sequencing was performed.", null, null, null, null, "darktreated2", null, "strain:not applicable|isolate:Sun Yat sen University|breed:not applicable2|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable2|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish2|isolation source:zebrafish2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample info", "library 2", "library 2", "DNA barcode2", null, null, "WXS", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP559934", null, null, "darktreated2.read1.fastq.gz darktreated2.read2.fastq.gz", "fastq fastq", 8723972700.0, 29079909.0, "darktreated2.read1.fastq.gz", "0:150 1:150", "A:2341340036;C:2009282478;G:2082163796;T:2291135873;N:50517", 150, 150, null, null, 2341340036, 2009282478, 2082163796, 2291135873, 50517, "SRX27475151", "SRS23899201", "SRA2060897", "zhujiang hospital|ophthalmology", "zhujiang hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-25", "Undetermined", "Adult", "Undetermined", "Undetermined"], [34604, "SRR32128868", "SRX27475150", "SRS23899200", "SRP559934", "PRJNA1215774", "3 mpf dark reared zebrafish eye RNA sequencing", "PRJNA1215774", "Other", "Outdoor time and light intensity are important emerging factors affecting myopia; however  the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment  3 mpf zebrafish eye RNA sequencing was performed.", null, null, null, null, "darktreated1", null, "strain:not applicable|isolate:Sun Yat sen University|breed:not applicable1|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable1|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish1|isolation source:zebrafish1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample info", "library 1", "library 1", "DNA barcode1", null, null, "WXS", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP559934", null, null, "darktreated1.read1.fastq.gz darktreated1.read2.fastq.gz", "fastq fastq", 7940928300.0, 26469761.0, "darktreated1.read1.fastq.gz", "0:150 1:150", "A:2133717650;C:1824526059;G:1895330033;T:2087310578;N:43980", 150, 150, null, null, 2133717650, 1824526059, 1895330033, 2087310578, 43980, "SRX27475150", "SRS23899200", "SRA2060897", "zhujiang hospital|ophthalmology", "zhujiang hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-25", "Undetermined", "Adult", "Undetermined", "Undetermined"], [34807, "SRR32289929", "SRX27626974", "SRS24034243", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 14dpi biological replicate 6", "GSM8784941", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 14dpi biological replicate 6", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2", "GSM8784941", "GSM8784941: FAC sorted RGCs at 14dpi biological replicate 6; Danio rerio; RNA Seq", "GSM8784941 r1", "GSM8784941", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC122375.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 455140014.0, 8924314.0, "GSM8784941 r1", "0:51", "A:121395551;C:104372745;G:106322577;T:123006247;N:42894", 51, null, null, null, 121395551, 104372745, 106322577, 123006247, 42894, "SRX27626974", "SRS24034243", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34808, "SRR32289930", "SRX27626974", "SRS24034243", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 14dpi biological replicate 6", "GSM8784941", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 14dpi biological replicate 6", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2", "GSM8784941", "GSM8784941: FAC sorted RGCs at 14dpi biological replicate 6; Danio rerio; RNA Seq", "GSM8784941 r1", "GSM8784941", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC122375.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 466246080.0, 9142080.0, "GSM8784941 r2", "0:51", "A:124363664;C:106868642;G:108780226;T:126189949;N:43599", 51, null, null, null, 124363664, 106868642, 108780226, 126189949, 43599, "SRX27626974", "SRS24034243", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34809, "SRR32289931", "SRX27626973", "SRS24034241", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 14dpi biological replicate 5", "GSM8784940", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 14dpi biological replicate 5", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2", "GSM8784940", "GSM8784940: FAC sorted RGCs at 14dpi biological replicate 5; Danio rerio; RNA Seq", "GSM8784940 r1", "GSM8784940", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC121325.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 453422589.0, 8890639.0, "GSM8784940 r1", "0:51", "A:119318402;C:105882527;G:107813042;T:120365525;N:43093", 51, null, null, null, 119318402, 105882527, 107813042, 120365525, 43093, "SRX27626973", "SRS24034241", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34810, "SRR32289932", "SRX27626973", "SRS24034241", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 14dpi biological replicate 5", "GSM8784940", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 14dpi biological replicate 5", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2", "GSM8784940", "GSM8784940: FAC sorted RGCs at 14dpi biological replicate 5; Danio rerio; RNA Seq", "GSM8784940 r1", "GSM8784940", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC121325.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 464612040.0, 9110040.0, "GSM8784940 r2", "0:51", "A:122313464;C:108440796;G:110356081;T:123457974;N:43725", 51, null, null, null, 122313464, 108440796, 110356081, 123457974, 43725, "SRX27626973", "SRS24034241", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34811, "SRR32289933", "SRX27626972", "SRS24034242", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 14dpi biological replicate 4", "GSM8784939", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 14dpi biological replicate 4", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2", "GSM8784939", "GSM8784939: FAC sorted RGCs at 14dpi biological replicate 4; Danio rerio; RNA Seq", "GSM8784939 r1", "GSM8784939", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC121324.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 399194493.0, 7827343.0, "GSM8784939 r1", "0:51", "A:104203040;C:94204942;G:95935068;T:104813749;N:37694", 51, null, null, null, 104203040, 94204942, 95935068, 104813749, 37694, "SRX27626972", "SRS24034242", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34812, "SRR32289934", "SRX27626972", "SRS24034242", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 14dpi biological replicate 4", "GSM8784939", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 14dpi biological replicate 4", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2", "GSM8784939", "GSM8784939: FAC sorted RGCs at 14dpi biological replicate 4; Danio rerio; RNA Seq", "GSM8784939 r1", "GSM8784939", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC121324.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 407414775.0, 7988525.0, "GSM8784939 r2", "0:51", "A:106355289;C:96099106;G:97825197;T:107096823;N:38360", 51, null, null, null, 106355289, 96099106, 97825197, 107096823, 38360, "SRX27626972", "SRS24034242", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34813, "SRR32289935", "SRX27626971", "SRS24034240", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 14dpi biological replicate 3", "GSM8784938", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 14dpi biological replicate 3", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2", "GSM8784938", "GSM8784938: FAC sorted RGCs at 14dpi biological replicate 3; Danio rerio; RNA Seq", "GSM8784938 r1", "GSM8784938", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC121323.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 393819042.0, 7721942.0, "GSM8784938 r1", "0:51", "A:104716428;C:90712029;G:92875673;T:105476998;N:37914", 51, null, null, null, 104716428, 90712029, 92875673, 105476998, 37914, "SRX27626971", "SRS24034240", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34814, "SRR32289936", "SRX27626971", "SRS24034240", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 14dpi biological replicate 3", "GSM8784938", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 14dpi biological replicate 3", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2", "GSM8784938", "GSM8784938: FAC sorted RGCs at 14dpi biological replicate 3; Danio rerio; RNA Seq", "GSM8784938 r1", "GSM8784938", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC121323.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 404191065.0, 7925315.0, "GSM8784938 r2", "0:51", "A:107484459;C:93060010;G:95238340;T:108369497;N:38759", 51, null, null, null, 107484459, 93060010, 95238340, 108369497, 38759, "SRX27626971", "SRS24034240", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34815, "SRR32289937", "SRX27626970", "SRS24034239", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 14dpi biological replicate 2", "GSM8784937", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 14dpi biological replicate 2", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1", "GSM8784937", "GSM8784937: FAC sorted RGCs at 14dpi biological replicate 2; Danio rerio; RNA Seq", "GSM8784937 r1", "GSM8784937", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC121322.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 387042774.0, 7589074.0, "GSM8784937 r1", "0:51", "A:107517102;C:84333044;G:85962742;T:109191597;N:38289", 51, null, null, null, 107517102, 84333044, 85962742, 109191597, 38289, "SRX27626970", "SRS24034239", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34816, "SRR32289938", "SRX27626970", "SRS24034239", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 14dpi biological replicate 2", "GSM8784937", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 14dpi biological replicate 2", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1", "GSM8784937", "GSM8784937: FAC sorted RGCs at 14dpi biological replicate 2; Danio rerio; RNA Seq", "GSM8784937 r1", "GSM8784937", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC121322.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 399657012.0, 7836412.0, "GSM8784937 r2", "0:51", "A:111048661;C:86998697;G:88636677;T:112933522;N:39455", 51, null, null, null, 111048661, 86998697, 88636677, 112933522, 39455, "SRX27626970", "SRS24034239", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34817, "SRR32289939", "SRX27626969", "SRS24034236", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 14dpi biological replicate 1", "GSM8784936", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 14dpi biological replicate 1", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1", "GSM8784936", "GSM8784936: FAC sorted RGCs at 14dpi biological replicate 1; Danio rerio; RNA Seq", "GSM8784936 r1", "GSM8784936", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC121320.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 358289280.0, 7025280.0, "GSM8784936 r1", "0:51", "A:101071342;C:75109849;G:76553150;T:105519857;N:35082", 51, null, null, null, 101071342, 75109849, 76553150, 105519857, 35082, "SRX27626969", "SRS24034236", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34818, "SRR32289940", "SRX27626969", "SRS24034236", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 14dpi biological replicate 1", "GSM8784936", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 14dpi biological replicate 1", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1", "GSM8784936", "GSM8784936: FAC sorted RGCs at 14dpi biological replicate 1; Danio rerio; RNA Seq", "GSM8784936 r1", "GSM8784936", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC121320.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 370202625.0, 7258875.0, "GSM8784936 r2", "0:51", "A:104421674;C:77537410;G:79038293;T:109169570;N:35678", 51, null, null, null, 104421674, 77537410, 79038293, 109169570, 35678, "SRX27626969", "SRS24034236", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34819, "SRR32289941", "SRX27626968", "SRS24034237", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 10dpi biological replicate 5", "GSM8784935", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 10dpi biological replicate 5", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2", "GSM8784935", "GSM8784935: FAC sorted RGCs at 10dpi biological replicate 5; Danio rerio; RNA Seq", "GSM8784935 r1", "GSM8784935", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC122374.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 403359306.0, 7909006.0, "GSM8784935 r1", "0:51", "A:104505636;C:95925686;G:97605050;T:105285164;N:37770", 51, null, null, null, 104505636, 95925686, 97605050, 105285164, 37770, "SRX27626968", "SRS24034237", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34820, "SRR32289942", "SRX27626968", "SRS24034237", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 10dpi biological replicate 5", "GSM8784935", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 10dpi biological replicate 5", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2", "GSM8784935", "GSM8784935: FAC sorted RGCs at 10dpi biological replicate 5; Danio rerio; RNA Seq", "GSM8784935 r1", "GSM8784935", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC122374.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 411821124.0, 8074924.0, "GSM8784935 r2", "0:51", "A:106698116;C:97949900;G:99548706;T:107586633;N:37769", 51, null, null, null, 106698116, 97949900, 99548706, 107586633, 37769, "SRX27626968", "SRS24034237", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34821, "SRR32289943", "SRX27626967", "SRS24034233", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 10dpi biological replicate 4", "GSM8784934", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 10dpi biological replicate 4", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2", "GSM8784934", "GSM8784934: FAC sorted RGCs at 10dpi biological replicate 4; Danio rerio; RNA Seq", "GSM8784934 r1", "GSM8784934", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC121319.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 320645415.0, 6287165.0, "GSM8784934 r1", "0:51", "A:83667318;C:75715675;G:77201096;T:84031268;N:30058", 51, null, null, null, 83667318, 75715675, 77201096, 84031268, 30058, "SRX27626967", "SRS24034233", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34822, "SRR32289944", "SRX27626967", "SRS24034233", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 10dpi biological replicate 4", "GSM8784934", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 10dpi biological replicate 4", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2", "GSM8784934", "GSM8784934: FAC sorted RGCs at 10dpi biological replicate 4; Danio rerio; RNA Seq", "GSM8784934 r1", "GSM8784934", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC121319.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 326655969.0, 6405019.0, "GSM8784934 r2", "0:51", "A:85253239;C:77113202;G:78588132;T:85671193;N:30203", 51, null, null, null, 85253239, 77113202, 78588132, 85671193, 30203, "SRX27626967", "SRS24034233", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34823, "SRR32289945", "SRX27626966", "SRS24034235", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 10dpi biological replicate 3", "GSM8784933", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 10dpi biological replicate 3", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2", "GSM8784933", "GSM8784933: FAC sorted RGCs at 10dpi biological replicate 3; Danio rerio; RNA Seq", "GSM8784933 r1", "GSM8784933", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC121318.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 383772552.0, 7524952.0, "GSM8784933 r1", "0:51", "A:100725108;C:90120177;G:92143732;T:100747122;N:36413", 51, null, null, null, 100725108, 90120177, 92143732, 100747122, 36413, "SRX27626966", "SRS24034235", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34824, "SRR32289946", "SRX27626966", "SRS24034235", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 10dpi biological replicate 3", "GSM8784933", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 10dpi biological replicate 3", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2", "GSM8784933", "GSM8784933: FAC sorted RGCs at 10dpi biological replicate 3; Danio rerio; RNA Seq", "GSM8784933 r1", "GSM8784933", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC121318.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 392096007.0, 7688157.0, "GSM8784933 r2", "0:51", "A:102939588;C:92028680;G:94033209;T:103058157;N:36373", 51, null, null, null, 102939588, 92028680, 94033209, 103058157, 36373, "SRX27626966", "SRS24034235", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34825, "SRR32289947", "SRX27626965", "SRS24034238", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 10dpi biological replicate 2", "GSM8784932", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 10dpi biological replicate 2", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2", "GSM8784932", "GSM8784932: FAC sorted RGCs at 10dpi biological replicate 2; Danio rerio; RNA Seq", "GSM8784932 r1", "GSM8784932", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC121317.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 396699216.0, 7778416.0, "GSM8784932 r1", "0:51", "A:103913407;C:93411140;G:95295922;T:104041015;N:37732", 51, null, null, null, 103913407, 93411140, 95295922, 104041015, 37732, "SRX27626965", "SRS24034238", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34826, "SRR32289948", "SRX27626965", "SRS24034238", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 10dpi biological replicate 2", "GSM8784932", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 10dpi biological replicate 2", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2", "GSM8784932", "GSM8784932: FAC sorted RGCs at 10dpi biological replicate 2; Danio rerio; RNA Seq", "GSM8784932 r1", "GSM8784932", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC121317.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 407433696.0, 7988896.0, "GSM8784932 r2", "0:51", "A:106734482;C:95879695;G:97797451;T:106984011;N:38057", 51, null, null, null, 106734482, 95879695, 97797451, 106984011, 38057, "SRX27626965", "SRS24034238", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34827, "SRR32289949", "SRX27626964", "SRS24034232", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 10dpi biological replicate 1", "GSM8784931", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 10dpi biological replicate 1", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1", "GSM8784931", "GSM8784931: FAC sorted RGCs at 10dpi biological replicate 1; Danio rerio; RNA Seq", "GSM8784931 r1", "GSM8784931", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC121316.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 357420852.0, 7008252.0, "GSM8784931 r1", "0:51", "A:100707954;C:76739501;G:77474055;T:102464781;N:34561", 51, null, null, null, 100707954, 76739501, 77474055, 102464781, 34561, "SRX27626964", "SRS24034232", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34828, "SRR32289950", "SRX27626964", "SRS24034232", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 10dpi biological replicate 1", "GSM8784931", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 10dpi biological replicate 1", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1", "GSM8784931", "GSM8784931: FAC sorted RGCs at 10dpi biological replicate 1; Danio rerio; RNA Seq", "GSM8784931 r1", "GSM8784931", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC121316.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 369272181.0, 7240631.0, "GSM8784931 r2", "0:51", "A:104043292;C:79231475;G:79962686;T:105999425;N:35303", 51, null, null, null, 104043292, 79231475, 79962686, 105999425, 35303, "SRX27626964", "SRS24034232", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34829, "SRR32289951", "SRX27626963", "SRS24034234", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 6dpi biological replicate 5", "GSM8784930", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 6dpi biological replicate 5", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2", "GSM8784930", "GSM8784930: FAC sorted RGCs at 6dpi biological replicate 5; Danio rerio; RNA Seq", "GSM8784930 r1", "GSM8784930", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC122373.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 383701101.0, 7523551.0, "GSM8784930 r1", "0:51", "A:101986811;C:88337442;G:89758931;T:103581971;N:35946", 51, null, null, null, 101986811, 88337442, 89758931, 103581971, 35946, "SRX27626963", "SRS24034234", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34830, "SRR32289952", "SRX27626963", "SRS24034234", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 6dpi biological replicate 5", "GSM8784930", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 6dpi biological replicate 5", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2", "GSM8784930", "GSM8784930: FAC sorted RGCs at 6dpi biological replicate 5; Danio rerio; RNA Seq", "GSM8784930 r1", "GSM8784930", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC122373.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 394847355.0, 7742105.0, "GSM8784930 r2", "0:51", "A:104937168;C:90871625;G:92274823;T:106726849;N:36890", 51, null, null, null, 104937168, 90871625, 92274823, 106726849, 36890, "SRX27626963", "SRS24034234", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34831, "SRR32289953", "SRX27626962", "SRS24034230", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 6dpi biological replicate 4", "GSM8784929", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 6dpi biological replicate 4", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2", "GSM8784929", "GSM8784929: FAC sorted RGCs at 6dpi biological replicate 4; Danio rerio; RNA Seq", "GSM8784929 r1", "GSM8784929", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC121313.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 397357269.0, 7791319.0, "GSM8784929 r1", "0:51", "A:102962865;C:94382913;G:96076584;T:103896489;N:38418", 51, null, null, null, 102962865, 94382913, 96076584, 103896489, 38418, "SRX27626962", "SRS24034230", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34832, "SRR32289954", "SRX27626962", "SRS24034230", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 6dpi biological replicate 4", "GSM8784929", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 6dpi biological replicate 4", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2", "GSM8784929", "GSM8784929: FAC sorted RGCs at 6dpi biological replicate 4; Danio rerio; RNA Seq", "GSM8784929 r1", "GSM8784929", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC121313.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 407641317.0, 7992967.0, "GSM8784929 r2", "0:51", "A:105635966;C:96802890;G:98458161;T:106705494;N:38806", 51, null, null, null, 105635966, 96802890, 98458161, 106705494, 38806, "SRX27626962", "SRS24034230", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory System"], [34833, "SRR32289955", "SRX27626961", "SRS24034228", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 6dpi biological replicate 3", "GSM8784928", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 6dpi biological replicate 3", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. 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tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation\" = :p0 and \"devstage_curation_coarse\" = :p1 order by rowid limit 101", "params": {"p0": "Undetermined", "p1": "Adult"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&devstage_curation_coarse=Adult", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 1157, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&devstage_curation_coarse=Adult&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "WXS", "label": "WXS", "count": 12, "toggle_url": 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"label": "PCR", "count": 24, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&devstage_curation_coarse=Adult&experiment.library_selection=PCR", "selected": false}, {"value": "RANDOM PCR", "label": "RANDOM PCR", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&devstage_curation_coarse=Adult&experiment.library_selection=RANDOM+PCR", "selected": false}, {"value": "size fractionation", "label": "size fractionation", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&devstage_curation_coarse=Adult&experiment.library_selection=size+fractionation", "selected": false}, {"value": "Oligo-dT", "label": "Oligo-dT", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&devstage_curation_coarse=Adult&experiment.library_selection=Oligo-dT", "selected": 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"toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&devstage_curation_coarse=Adult&experiment.platform=ABI_SOLID", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&devstage_curation_coarse=Adult", "results": [{"value": "Adult", "label": "Adult", "count": 1179, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined", "selected": true}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&devstage_curation_coarse=Adult", "results": [{"value": "Undetermined", "label": "Undetermined", "count": 1179, "toggle_url": 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